Difference between revisions of "2025 DOCK tutorial 1 with PDBID 1O86"

Revision as of 12:36, 21 February 2025

1 DOCK Tutorial using PDB 1O86
2 000: Foundations
- 2.1 Chimera
3 001: Structure Prep
4 002: Spheres
5 003: Grid/box
6 004: Minimization
7 005: Rigid Docking
8 006: Flexible Docking
9 007: Footprint Scoring
10 008: 5k Virtual Screen
11 009: Genetic Algorithm Example
12 010: De Novo Design Example
13 > WARNING: A newer version of conda exists. <

DOCK Tutorial using PDB 1O86

[intro text]

000: Foundations

Chimera

UCSF Chimera is a python-based, open-source molecular visualization and manipulation software suite. It is extremely helpful for both preparing molecules/receptors for docking and for visually analyzing the results of those calculations.

It can be downloaded from the official UCSF site; make sure to select the version that matches your operating system (Mac or Windows). Although Chimera is no longer under active development, it remains a relevant software for molecular modeling.

Once Chimera has installed, you can open it to find a blank blue-ish window, with a row of tabs along the top. Throughout this tutorial, you will be instructed to perform different actions contained within these tabs. We will denote the specific tab and sub-tab to be accessed by >> signs. For example, File >> Open PDB would indicate that you should click on the File tab, then mouse to and click Open PDB. This is necessary because some actions are nested in multiple sub-tabs (for instance, selecting all hydrogens in a model would require Select >> Chemistry >> element >> H, as shown below) More extensive documentation on Chimera and its functions is available on the official site.

001: Structure Prep

Download PDB, separate lig/rec, model loops, addH/charge

Downloading the PDB

Having setup your necessary environment to work on seawulf, lets navigate to your local computer and begin the protein preparation process:

To begin protein preparation you will need the necessary PDB file to work with. Using this link: https://www.rcsb.org/structure/1O86, you will see the RCSB main page opened to our protein of choice:

Next, you'll want to navigate to the top right corner where it says Download Files. Then, select the dropdown arrow. The following pulldown menu will appear on the screen:

Select 'Download PDB'. Now the PDB file is downloaded to your local computer.

Now that you have the PDB file, lets navigate to Chimera program to open the file.

002: Spheres

surface generation, sphgen, selecting spheres, visualization in Chimera

Generate the required surface file

1. Open 1O86 protein only file in chimera and hit select > show> surface 2. Write the DMS file by choosing tools>structure editing>Write DMS 3. Upload the DMS file to your directory 4. Create a sphere input file using the following command:

vi INSPH

5. Paste the following into your input file:

./IO86.dms
R
X
0.0
4.0
1.4
IO86.sph

6. Run the program with the following command

sphgen -i INSPH -o OUTSPH

7. Download the output file to your local directory and open and overlay with protein file in Chimera File:Screenshot 2025-02-19 130820.png

Based on the overlay the ribbons are aligned with the spheres indicating the generation of surface spheres was successful.

Generate Spheres localized on binding site

003: Grid/box

showbox, grid generation, visualization in Chimera

004: Minimization

Explanation of .in file for minimization and process (Chimera visuals after)

005: Rigid Docking

Explanation of .in file for rigid docking and process (Chimera visuals after)

006: Flexible Docking

Explanation of .in for flex docking (Chimera visuals after)

007: Footprint Scoring

Explanation of .in for FPS, use of Python script to generate graph

008: 5k Virtual Screen

Slurm and queue etiquette, VS .in explanation and queue submission, ViewDock in Chimera

009: Genetic Algorithm Example

Explanation of rationale for GA and basic functionality, sample input file and expected outputs

010: De Novo Design Example

Explanation of rationale for DN and basic functionality, sample input file and expected outputs

De Novo Design is a dock based algorithm that generates new ligands from scratch. This is done by selecting a dummy atom, which is the 'seed' that 'grows' scaffolds, linkers, or side chains based on user defined parameters. For example, say you only wanted to use de novo design to only 'grow' drug-like molecules. The way this is accomplished is ensuring the input file contains parameters that bias the algorithm to abide by Lipinski's Rule of 5 The guiding principle for using De Novo design is because there is a limit to the amount of new molecules that you could generate using a general virtual screening. Nevertheless, this method will certainly aid in enhancing your search space in generating numerous new compounds.

Selecting a Dummy Atom

To prepare our molecule for a De Novo calculation, we must first select a dummy atom to 'grow' from. To do this, first open your 1O86_fixed_protein_H_cH.mol2 file, then your 1O86_ligand_H_cH.mol2. The rationale for this is we would like to delete an atom on the ligand that contains a group that interacts with the protein. This will help to produce meaningful results, from a drug design standpoint:

As you can see it is a little difficult to see which atoms are interacting with the protein. To refine this inspection, hit Control and select an atom on the ligand. Then, hit the up arrow to highlight the entire ligand. Next, hit Select --> Zone and the following menu appears:

Lets modify the Zone and change the number from 5.0 angstroms to 3.0 angstroms. Additionally, make sure that that the third box is checked off entitled that selects neighboring residues. Then, press okay. You will notice that your ligand and the neighboring residues are highlighted:

To modify this image even further: Go to Actions --> Atoms/Bonds --> hit Show Next, navigate to Select --> press Invert(selected models), here you'll notice most of the protein is highlighted Lastly, Return to Actions --> Atoms/Bonds --> hit delete You now see that there is a clearer picture of specifically, which atoms are interacting closely with the protein

You'll notice that there are two oxygens interacting with neighboring residues in the protein. Tracing your cursor in between the oxygens, you'll highlight a Carbon atom labeled C9. This will be the atom of choice for this tutorial.

Generating a Dummy Atom

Now that we have our atom of choice, we need to modify the ligand as well as the mol2 file itself.

First, open the 1O86_ligand_H_cH.mol2 in Chimera.

Locate the C9 atom --> select the two oxygens attached to C9 --> Atoms/Bonds --> delete. Then, save the mol2 file, lets call it 1O86_ligand_Du.mol2.

Finally, we must open the mol2 file on our terminal and change the atom type of C9 to Du:

First in the terminal, type the command

vi 1O86_ligand_Du.mol2

Find the C9 atom and modify the atom type. Your input file should look like this:

Save it.

Now lets verify this change by opening the mol2 file on Chimera:

As you can see C5 is now a dummy atom as shown in purple

Now, the mol2 is ready for De Novo calculations

As a last step, transfer the mol2 to your working directory on seawulf

scp 1O86_ligand_Du.mol2 username@login.seawulf.stonybrook.edu:'/gpfs/username/010_de_novo'

Running The Denovo Calculation

In your 010_De_Novo folder create an empty input file:

touch DN.in

Then prompt the question tree with the dock program:

dock6 -i DN.in

Follow the question tree and use the following sample input file as a template

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(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ home (base) [ehspector@login1 espector]$ cd .. (base) [ehspector@login1 rizzo]$ cd .. 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(base) [ehspector@login1 2025]$ cd .. (base) [ehspector@login1 AMS536]$ cd 2025 (base) [ehspector@login1 2025]$ pwd /gpfs/projects/AMS536/2025 (base) [ehspector@login1 2025]$ vi ~/.bashrc (base) [ehspector@login1 2025]$ home (base) [ehspector@login1 espector]$ source ~/.bashrc (base) [ehspector@login1 espector]$ class (base) [ehspector@login1 2025]$ home (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ exit logout Connection to login.seawulf.stonybrook.edu closed. 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Methyl Red Excel.xlsx Movies Music NBA_players_2015.csv Overdue Customers 2.xlsx Oxamide_n2_water.agr Peer.ipynb Pictures Practice.ipynb Profile Picture.jpg Project.ipynb Prototype.ipynb Prototype_5.ipynb Public Quiz Review.ipynb README.md Reaction 1 Data.xlsx Reaction 2 Data.xlsx Reaction 3 Data.xlsx Reaction 4 Data.xlsx Red Cross - Wallet Card - Individual_SD-37055011.pdf Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf Review Lab_ Evan S..ipynb Review3_EvanS.ipynb Review_2.ipynb SAT__College_Board__2010_School_Level_Results.csv Sine and Cosine Curve.ipynb Split_2.tga SpotifyFinalProject.ipynb SulfurCys.agr TSLA.csv UNL.agr Untitled Folder Untitled.ipynb Untitled1.ipynb Untitled2.ipynb WAT_O.agr Working with OpenPyXL.xlsx anaconda3 eclipse eclipse-workspace final_project_draft4.ipynb helloWorld.py install.sh introdata.ipynb java.log.34001 java.log.37118 job_skills.csv jupyter_mac.command matlab_crash_dump.6196-1 miniconda3 multiplot.agr opt plotting-with-pandas.ipynb population-by-country-2020.zip population_by_country_2020.csv rmsd.agr source.venv test.encrypted test.txt twitter-workshop-master.zip (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ home (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd 4s0v/ (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ cd no_charge/ (base) [ehspector@login1 no_charge]$ ls 4s0v_no_hydrogens_no_charges.mol2 gas_2.in gas_2.out gas.out_scored.mol2 (base) [ehspector@login1 no_charge]$ cd .. (base) [ehspector@login1 gas_teiger]$ vi no_gas.in (base) [ehspector@login1 gas_teiger]$ vi no_gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ cd .. (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd GA_data/ (base) [ehspector@login1 GA_data]$ ls First_gen_data Last_gen_data (base) [ehspector@login1 GA_data]$ cd .. (base) [ehspector@login1 4s0v]$ cd gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ home (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd gas_test/ (base) [ehspector@login1 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@login1 gas_test]$ cd .. (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd 4s0v/ (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd s -bash: cd: s: No such file or directory (base) [ehspector@login1 4s0v]$ cd structure/ (base) [ehspector@login1 structure]$ ls 4s0v_ligand_hydrogens_charges.mol2 4s0v_no_hydrogens_no_charges.mol2 4s0v_ligand_no_hydrogens_no_charges.mol2 4s0v_protein_with_charges.mol2 (base) [ehspector@login1 structure]$ cd .. (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd .. (base) [ehspector@login1 espector]$ cd gas_test/ (base) [ehspector@login1 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@login1 gas_test]$ cd gas_f_test/ (base) [ehspector@login1 gas_f_test]$ ls diff.out gas_0.out_scored.mol2 gas_1.out gas_50.in gas_50.out_scored.mol2 gas_0.out gas_1.in gas_1.out_scored.mol2 gas_50.out (base) [ehspector@login1 gas_f_test]$ vi gas_1.in (base) [ehspector@login1 gas_f_test]$ cd .. (base) [ehspector@login1 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@login1 gas_test]$ cd .. (base) [ehspector@login1 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ module Modules Release 4.0.0 (2017-10-16) Usage: module [options] [command] [args ...]

Loading / Unloading commands:

 add | load      modulefile [...]  Load modulefile(s)
 rm | unload     modulefile [...]  Remove modulefile(s)
 purge                             Unload all loaded modulefiles
 reload | refresh                  Unload then load all loaded modulefiles
 switch | swap   [mod1] mod2       Unload mod1 and load mod2

Listing / Searching commands:

 list            [-t|-l]           List loaded modules
 avail   [-d|-L] [-t|-l] [mod ...] List all or matching available modules
 aliases                           List all module aliases
 whatis          [modulefile ...]  Print whatis information of modulefile(s)
 apropos | keyword | search  str   Search all name and whatis containing str

Collection of modules handling commands:

 save            [collection|file] Save current module list to collection
 restore         [collection|file] Restore module list from collection or file
 saverm          [collection]      Remove saved collection
 saveshow        [collection|file] Display information about collection
 savelist        [-t|-l]           List all saved collections

Shell's initialization files handling commands:

 initlist                          List all modules loaded from init file
 initadd         modulefile [...]  Add modulefile to shell init file
 initrm          modulefile [...]  Remove modulefile from shell init file
 initprepend     modulefile [...]  Add to beginning of list in init file
 initswitch      mod1 mod2         Switch mod1 with mod2 from init file
 initclear                         Clear all modulefiles from init file

Other commands:

 help            [modulefile ...]  Print this or modulefile(s) help info
 display | show  modulefile [...]  Display information about modulefile(s)
 test            [modulefile ...]  Test modulefile(s)
 use     [-a|-p] dir [...]         Add dir(s) to MODULEPATH variable
 unuse           dir [...]         Remove dir(s) from MODULEPATH variable
 path            modulefile        Print modulefile path
 paths           modulefile        Print path of matching available modules
 source          scriptfile [...]  Execute scriptfile(s)

Switches:

 -t | --terse    Display output in terse format
 -l | --long     Display output in long format
 -d | --default  Only show default versions available
 -L | --latest   Only show latest versions available
 -a | --append   Append directory to MODULEPATH
 -p | --prepend  Prepend directory to MODULEPATH

Options:

 -h | --help     This usage info
 -V | --version  Module version
 -D | --debug    Enable debug messages

(base) [ehspector@login1 gas_teiger]$ module list Currently Loaded Modulefiles:

1) slurm/17.11.12   2) shared

(base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ cd .. (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd structure/ (base) [ehspector@login1 structure]$ ls 4s0v_ligand_hydrogens_charges.mol2 4s0v_no_hydrogens_no_charges.mol2 4s0v_ligand_no_hydrogens_no_charges.mol2 4s0v_protein_with_charges.mol2 (base) [ehspector@login1 structure]$ cd .. (base) [ehspector@login1 4s0v]$ cd gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ cd .. (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ vi gas_teiger/ (base) [ehspector@login1 4s0v]$ cd gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ cd .. (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd energy_min/ (base) [ehspector@login1 energy_min]$ ls 4s0v.lig.min_scored.mol2 min.in min.out (base) [ehspector@login1 energy_min]$ cd .. (base) [ehspector@login1 4s0v]$ cd .. (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd 4s0v/ (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ vi gas_teiger/ (base) [ehspector@login1 4s0v]$ cd gas_teiger/ (base) [ehspector@login1 gas_teiger]$ vi gas. (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ cd .. (base) [ehspector@login1 4s0v]$ cd surface_spheres/ (base) [ehspector@login1 surface_spheres]$ ls 4s0v_binding_spheres.sph 4s0v_surface.dms INSPH OUTSPH selected_spheres.sph (base) [ehspector@login1 surface_spheres]$ cd .. (base) [ehspector@login1 4s0v]$ cd .. (base) [ehspector@login1 espector]$ cd gas_test/ (base) [ehspector@login1 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@login1 gas_test]$ cd .. (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd 4s0v/ (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd surface_spheres/ (base) [ehspector@login1 surface_spheres]$ ls 4s0v_binding_spheres.sph 4s0v_surface.dms INSPH OUTSPH selected_spheres.sph (base) [ehspector@login1 surface_spheres]$ cd .. (base) [ehspector@login1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login1 4s0v]$ cd gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out (base) [ehspector@login1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ class (base) [ehspector@login2 2025]$ ls additional_files (base) [ehspector@login2 2025]$ cd additional_files/ (base) [ehspector@login2 additional_files]$ ls sample_bashrc_4seawulf.txt sample_slurm_submission.sh touch.sh (base) [ehspector@login2 additional_files]$ vi sample_bashrc_4seawulf.txt (base) [ehspector@login2 additional_files]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login2 espector]$ cd builds/ (base) [ehspector@login2 builds]$ cd alpha_branch/ (base) [ehspector@login2 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@login2 alpha_branch]$ cd install/ (base) [ehspector@login2 install]$ ls bluegenel gnu.acml homebrew intel.mkl sgi bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel config.h gnu.parallel ibmaix Makefile test configure gnu.parallel.rdkit intel oneapi docker gnu.rdkit intel.intelmpi.parallel pgi gnu gnu.valgrind intel.ip.mkl rules.h (base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ l bash: l: command not found... (base) [ehspector@login2 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@login2 alpha_branch]$ cd install/ (base) [ehspector@login2 install]$ ls bluegenel gnu.acml homebrew intel.mkl sgi bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel config.h gnu.parallel ibmaix Makefile test configure gnu.parallel.rdkit intel oneapi docker gnu.rdkit intel.intelmpi.parallel pgi gnu gnu.valgrind intel.ip.mkl rules.h (base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@login2 alpha_branch]$ cd bin/ (base) [ehspector@login2 bin]$ ls dock6 dock6.rdkit (base) [ehspector@login2 bin]$ vi dock6.rdkit (base) [ehspector@login2 bin]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd src/ (base) [ehspector@login2 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@login2 src]$ vi Makefile (base) [ehspector@login2 src]$ cd rdkit/ (base) [ehspector@login2 rdkit]$ ls boost boost_1_71_0.tar.gz eigen-3.3.9.tar.gz rdkit-Release_2019_09_1 boost_1_71_0 eigen-3.3.9 Makefile rdkit-Release_2019_09_1.tar.gz (base) [ehspector@login2 rdkit]$ vi Makefile (base) [ehspector@login2 rdkit]$ vi Makefile (base) [ehspector@login2 rdkit]$ vi Makefile (base) [ehspector@login2 rdkit]$ ls boost boost_1_71_0.tar.gz eigen-3.3.9.tar.gz rdkit-Release_2019_09_1 boost_1_71_0 eigen-3.3.9 Makefile rdkit-Release_2019_09_1.tar.gz (base) [ehspector@login2 rdkit]$ module list Currently Loaded Modulefiles:

1) slurm/17.11.12   2) shared

(base) [ehspector@login2 rdkit]$ module load git WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.

/cm/local/apps/environment-modules/4.0.0//bin

(base) [ehspector@login2 rdkit]$ module list Currently Loaded Modulefiles:

1) slurm/17.11.12   2) shared   3) git/2.36.2

(base) [ehspector@login2 rdkit]$ git branch

alpha_branch

 master

(base) [ehspector@login2 rdkit]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25 (base) supremestudier@Evans-MBP Spring_25 % ls AMS_500 AMS_537 AMS_691 AMS_536 AMS_548 CARS_551 (base) supremestudier@Evans-MBP Spring_25 % cd AMS_691 (base) supremestudier@Evans-MBP AMS_691 % ls AMS691_01.pdf Projects Text_book (base) supremestudier@Evans-MBP AMS_691 % mkdir Lectures (base) supremestudier@Evans-MBP AMS_691 % cd .. (base) supremestudier@Evans-MBP Spring_25 % cd AMS_500 (base) supremestudier@Evans-MBP AMS_500 % ls 2010.06.08_hadjiargyrou.pdf (base) supremestudier@Evans-MBP AMS_500 % mkdir Materials (base) supremestudier@Evans-MBP AMS_500 % mv 2010.06.08_hadjiargyrou.pdf Materials (base) supremestudier@Evans-MBP AMS_500 % ls Materials (base) supremestudier@Evans-MBP AMS_500 % cd .. (base) supremestudier@Evans-MBP Spring_25 % cd CARS_551 (base) supremestudier@Evans-MBP CARS_551 % ls (base) supremestudier@Evans-MBP CARS_551 % cd .. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login2 espector]$ cd gas_test/ (base) [ehspector@login2 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@login2 gas_test]$ cd .. (base) [ehspector@login2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login2 espector]$ cd 4s0v/ (base) [ehspector@login2 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login2 4s0v]$ cd structure/ (base) [ehspector@login2 structure]$ ls 4s0v_ligand_hydrogens_charges.mol2 4s0v_no_hydrogens_no_charges.mol2 4s0v_ligand_no_hydrogens_no_charges.mol2 4s0v_protein_with_charges.mol2 (base) [ehspector@login2 structure]$ cd .. (base) [ehspector@login2 4s0v]$ cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/ (base) [ehspector@login2 4s0v]$ cd gas_teiger/ (base) [ehspector@login2 gas_teiger]$ ls 4s0v_ligand_hydrogens_charges.mol2 gas.out no_charge no_gas.out gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2 (base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2 (base) [ehspector@login2 gas_teiger]$ pwd /gpfs/projects/rizzo/espector/4s0v/gas_teiger (base) [ehspector@login2 gas_teiger]$ ls 4s0v_ligand_hydrogens_charges.mol2 gas.out no_charge no_gas.out gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ cd no_charge/ (base) [ehspector@login2 no_charge]$ ls 4s0v_no_hydrogens_no_charges.mol2 gas_2.in gas_2.out gas.out_scored.mol2 (base) [ehspector@login2 no_charge]$ vi gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ cd .. (base) [ehspector@login2 gas_teiger]$ mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/ (base) [ehspector@login2 gas_teiger]$ cd no_charge/ (base) [ehspector@login2 no_charge]$ ls 4s0v_ligand_hydrogens_charges.mol2 gas_2.in gas.out_scored.mol2 4s0v_no_hydrogens_no_charges.mol2 gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@login2 no_charge]$ ls 4s0v_ligand_hydrogens_charges.mol2 gas_2.in gas.out_scored.mol2 4s0v_no_hydrogens_no_charges.mol2 gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@login2 no_charge]$ ls 4s0v_ligand_hydrogens_charges.mol2 gas_2.in gas.out_scored.mol2 4s0v_no_hydrogens_no_charges.mol2 gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.out (base) [ehspector@login2 no_charge]$ mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2 (base) [ehspector@login2 no_charge]$ ls 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in gas.out_scored.mol2 4s0v_no_hydrogens_no_charges.mol2 gas_2.out (base) [ehspector@login2 no_charge]$ cd .. (base) [ehspector@login2 gas_teiger]$ cd .. (base) [ehspector@login2 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/ (base) [ehspector@login2 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/ (base) [ehspector@login2 no_charge]$ ls 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in 4s0v.lig.min_scored.mol2 gas_2.out 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2 (base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2 (base) [ehspector@login2 no_charge]$ vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2 2 files to edit (base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2 (base) [ehspector@login2 no_charge]$ mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2 (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@login2 no_charge]$ ls 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in 4s0v.lig_no_charge.min_scored.mol2 gas_2.out 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2 (base) [ehspector@login2 no_charge]$ vi gas_2.out (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ vi gas.out_scored.mol2 (base) [ehspector@login2 no_charge]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ cd 4s0v/ (base) [ehspector@login2 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/ (base) [ehspector@login2 no_charge]$ vi gas_2.in (base) [ehspector@login2 no_charge]$ vi 4s0v.lig_no_charge.min_scored.mol2 (base) [ehspector@login2 no_charge]$ vi gas_2.out (base) [ehspector@login2 no_charge]$ cd .. (base) [ehspector@login2 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login2 gas_teiger]$ vi gas.in (base) [ehspector@login2 gas_teiger]$ vi gas.out (base) [ehspector@login2 gas_teiger]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login2 espector]$ cd 4s0v/ (base) [ehspector@login2 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@login2 4s0v]$ cd gas_teiger/ (base) [ehspector@login2 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@login2 gas_teiger]$ vi no_gas.in (base) [ehspector@login2 gas_teiger]$ vi no_gas.out (base) [ehspector@login2 gas_teiger]$ vi no_gas.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ class (base) [ehspector@login1 2025]$ pwd /gpfs/projects/AMS536/2025 (base) [ehspector@login1 2025]$ cd .. (base) [ehspector@login1 AMS536]$ vi ~/.bashrc (base) [ehspector@login1 AMS536]$ source ~/.bashrc WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.

/cm/local/apps/environment-modules/4.0.0//bin

(base) [ehspector@login1 AMS536]$ home (base) [ehspector@login1 espector]$ class (base) [ehspector@login1 2025]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % tutor zsh: command not found: tutor (base) supremestudier@Evans-MBP Spring_25 % vimtutor (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ class (base) [ehspector@login2 2025]$ mkdir ehspector mkdir: cannot create directory ‘ehspector’: Permission denied (base) [ehspector@login2 2025]$ mkdir ehspector (base) [ehspector@login2 2025]$ ls additional_files ehspector ooreilly (base) [ehspector@login2 2025]$ cd ehspector/ (base) [ehspector@login2 ehspector]$ ls (base) [ehspector@login2 ehspector]$ touch file.txt (base) [ehspector@login2 ehspector]$ ls (base) [ehspector@login2 ehspector]$ cd .. (base) [ehspector@login2 2025]$ cd .. (base) [ehspector@login2 AMS536]$ cd (base) [ehspector@login2 ~]$ ls miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@login2 ~]$ mkdir class_project (base) [ehspector@login2 ~]$ ls class_project miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@login2 ~]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ssh: connect to host login.seawulf.stonybrook.edu port 22: Undefined error: 0 (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ home (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd builds/ (base) [ehspector@login1 builds]$ ls alpha_branch dock6-master dock6-master.zip dock6-rdkit (base) [ehspector@login1 builds]$ cd alpha_branch/ (base) [ehspector@login1 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@login1 alpha_branch]$ module load git WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.

/cm/local/apps/environment-modules/4.0.0//bin

(base) [ehspector@login1 alpha_branch]$ git branch

alpha_branch

 master

(base) [ehspector@login1 alpha_branch]$ git config --get remote.origin.url https://github.com/EvanS-Dock6/dock6.git (base) [ehspector@login1 alpha_branch]$ git pull Username for 'https://github.com': EvanS_Dock6 Password for 'https://EvanS_Dock6@github.com': remote: Support for password authentication was removed on August 13, 2021. remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication. fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/' (base) [ehspector@login1 alpha_branch]$ git pull Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': remote: Support for password authentication was removed on August 13, 2021. remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication. fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/' (base) [ehspector@login1 alpha_branch]$ git pull Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': remote: Enumerating objects: 1129, done. remote: Counting objects: 100% (672/672), done. remote: Compressing objects: 100% (147/147), done. remote: Total 1129 (delta 585), reused 561 (delta 525), pack-reused 457 (from 1) Receiving objects: 100% (1129/1129), 1.09 MiB | 13.11 MiB/s, done. Resolving deltas: 100% (909/909), completed with 45 local objects. From https://github.com/EvanS-Dock6/dock6

  4be5c842..2ce698b4  alpha_branch -> origin/alpha_branch
  50ce88e6..da80bfc9  master       -> origin/master

Updating 4be5c842..2ce698b4 error: Your local changes to the following files would be overwritten by merge: src/dock/dock.cpp src/dock/orient.cpp src/dock/sphere.cpp Please commit your changes or stash them before you merge. Aborting (base) [ehspector@login1 alpha_branch]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout modified: src/dock/dock.cpp modified: src/dock/filter.cpp modified: src/dock/filter.h modified: src/dock/gasteiger.cpp modified: src/dock/orient.cpp modified: src/dock/sphere.cpp modified: src/rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 alpha_branch]$ git diff src/dock/dock.cpp diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp index 81925eac..e447b601 100644 --- a/src/dock/dock.cpp +++ b/src/dock/dock.cpp @@ -820,7 +820,7 @@ main(int argc, char **argv)

        if (c_filter.use_database_filter)
        {
            //calculate RDKIT-related descriptors for the ligand

- c_filter.calc_descriptors(mol); + c_filter.calc_descriptors(mol, c_typer);

            //other descriptors are now computed & printed in amber_typer.cpp
            //print out the descriptors
            //cout << c_filter.get_descriptors(mol);

(base) [ehspector@login1 alpha_branch]$ git diff src/dock/gasteiger.cpp diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp index 5cfba835..3a967b89 100644 --- a/src/dock/gasteiger.cpp +++ b/src/dock/gasteiger.cpp @@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {

    //Fochmod
    //printf("gasteiger mark #1 \n");

- + cout << "The for loop is initiated" << endl;

    for (int a = 0; a < mol.num_atoms; a++) {
        //printf("switchloop %d  \n", a);
        switch (mol.atom_envs[a][1]) {

@@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {

                param_b[a]     = 9.18;
                param_c[a]     = 1.88;
                param_d[a]     = param_a[a] + param_b[a] + param_c[a];

+ cout << "This is the charge" << endl;

                break;
            case 'B':   //C.2  trtrtr pi
                tot_charges[a] = 0.0;

(base) [ehspector@login1 alpha_branch]$ git diff src/dock/orient.cpp diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp index 92d58f71..2d63fece 100644 --- a/src/dock/orient.cpp +++ b/src/dock/orient.cpp @@ -461,8 +461,7 @@ Orient::get_spheres()

    spheres = Active_Site_Spheres :: get_instance();
    num_spheres = spheres.size();

- if (verbose) cout << "Read in " << num_spheres - << " spheres for orienting." << endl; + cout << "Read in " << num_spheres << " spheres for orienting." << endl;

    // process critical points
    if (critical_points) {

(base) [ehspector@login1 alpha_branch]$ git diff src/dock/sphere.cpp diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp index 27641d83..5739a67c 100644 --- a/src/dock/sphere.cpp +++ b/src/dock/sphere.cpp @@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )

    fclose(sphere_file);

    return num_spheres;

+

(base) [ehspector@login1 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@login1 alpha_branch]$ cd src/dock (base) [ehspector@login1 dock]$ vi gasteiger.cpp (base) [ehspector@login1 dock]$ git diff gasteiger.cpp diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp index 5cfba835..3a967b89 100644 --- a/src/dock/gasteiger.cpp +++ b/src/dock/gasteiger.cpp @@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {

    //Fochmod
    //printf("gasteiger mark #1 \n");

- + cout << "The for loop is initiated" << endl;

    for (int a = 0; a < mol.num_atoms; a++) {
        //printf("switchloop %d  \n", a);
        switch (mol.atom_envs[a][1]) {

@@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {

                param_b[a]     = 9.18;
                param_c[a]     = 1.88;
                param_d[a]     = param_a[a] + param_b[a] + param_c[a];

+ cout << "This is the charge" << endl;

                break;
            case 'B':   //C.2  trtrtr pi
                tot_charges[a] = 0.0;

(base) [ehspector@login1 dock]$ vi gasteiger.cpp (base) [ehspector@login1 dock]$ git diff gasteiger.cpp diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp index 5cfba835..e82d5397 100644 --- a/src/dock/gasteiger.cpp +++ b/src/dock/gasteiger.cpp @@ -272,7 +272,6 @@ compute_gast_charges(DOCKMol & mol) {

    //Fochmod
    //printf("gasteiger mark #1 \n");

-

    for (int a = 0; a < mol.num_atoms; a++) {
        //printf("switchloop %d  \n", a);
        switch (mol.atom_envs[a][1]) {

(base) [ehspector@login1 dock]$ git status gasteiger.cpp On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

modified: gasteiger.cpp

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 dock]$ vi gasteiger.cpp (base) [ehspector@login1 dock]$ git diff gasteiger.cpp (base) [ehspector@login1 dock]$ git status gasteiger.cpp On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

nothing to commit, working tree clean (base) [ehspector@login1 dock]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: ../../install/test/minimization/minimize7.dockout modified: dock.cpp modified: filter.cpp modified: filter.h modified: orient.cpp modified: sphere.cpp modified: ../rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

lol ../rdkit/boost/ ../rdkit/boost_1_71_0.tar.gz ../rdkit/boost_1_71_0/ ../rdkit/eigen-3.3.9.tar.gz ../rdkit/eigen-3.3.9/ ../rdkit/rdkit-Release_2019_09_1.tar.gz ../rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 dock]$ git diff sphere.cpp diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp index 27641d83..5739a67c 100644 --- a/src/dock/sphere.cpp +++ b/src/dock/sphere.cpp @@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )

    fclose(sphere_file);

    return num_spheres;

+

(base) [ehspector@login1 dock]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % mkdir PHYS_561 (base) supremestudier@Evans-MBP Spring_25 % cd PHYS_561 (base) supremestudier@Evans-MBP PHYS_561 % mkdir Readings (base) supremestudier@Evans-MBP PHYS_561 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ class (base) [ehspector@login2 2025]$ cd (base) [ehspector@login2 ~]$ ls class_project miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@login2 ~]$ mv class_project/ AMS_536 (base) [ehspector@login2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@login2 ~]$ cd AMS_536/ (base) [ehspector@login2 AMS_536]$ ls (base) [ehspector@login2 AMS_536]$ mkdir class_work (base) [ehspector@login2 AMS_536]$ mkdir class_project (base) [ehspector@login2 AMS_536]$ cd .. (base) [ehspector@login2 ~]$ cd AMS_536/ (base) [ehspector@login2 AMS_536]$ pwd /gpfs/home/ehspector/AMS_536 (base) [ehspector@login2 AMS_536]$ vi ~/.bashrc (base) [ehspector@login2 AMS_536]$ source ~/.bashrc (base) [ehspector@login2 AMS_536]$ home (base) [ehspector@login2 espector]$ class (base) [ehspector@login2 AMS_536]$ ls class_project class_work (base) [ehspector@login2 AMS_536]$ ls class_project class_work (base) [ehspector@login2 AMS_536]$ pwd /gpfs/home/ehspector/AMS_536 (base) [ehspector@login2 AMS_536]$ cd .. (base) [ehspector@login2 ~]$ cd .. (base) [ehspector@login2 home]$ cd .. (base) [ehspector@login2 gpfs]$ cd projects/ (base) [ehspector@login2 projects]$ ls ABCD EssigGroup MaoGroup SchedelGroup AllamGroup FarhadzadehGroup McDonoughGroup SeeligerGroup AllenGroup FernandezGroup McGrewGroup SehgalGroup AMS530 FernandezReuterGroup McKinnonGroup ShepsonGroup AMS536 FrenkelGroup MehmoodGroup SherGroup AMS598 FutcherGroup MelikerGroup SheridanGroup AMS691 GenomicsCore MihalacheGroup ShilkrotGroup Aponte-RiveraGroup GergenGroup MirandaGroup SiegmannGroup ArmitageGroup glimm MitchellGroup SladeGroup AssanisGroup GoblerGroup MoellerGroup SmaersGroup BEE690 GoldbartGroup MofakhamGroup SOC591 BenchmarkGroup HCPGroup MohantyGroup SOC595 BenderGroup HeinzGroup MollProject StanacevicGroup BernauerGroup HollisterGroup molssi SternGroup BialkowskaGroup HoltGroup MoutsanidisGroup SyritsynGroup BIO303 hpc_support MujicaGroup TakeuchiGroup BluesteinGroup HudsonGroup NadkarniGroup TanGroup BurguenoGroup IACSPDPGroup NMRPIJodeyGroup TaylorGroup CalderGroup JiaoGroup NMRPILipshultzGroup TeraChemGroup CanliGroup JohnsonGroup NMRPIMingNgaiGroup Tesse CarlsonGroup JonesBozarthGroup NMRPIPicartGroup TestGroup1 CascanteBonillaGroup JonesGroup OjimaGroup ThackerGroup ChangGroup JonesSkienaGroup OkeomaGroup ThakurGroup ChapmanGroup KarzaiGroup PadillaGroup ThorneGroup CheCastaldoGroup KeeGroup PariseGroup TitleGroup ChenGroup KeeJiaoGroup PercivalGroup TsybychevGroup ChenXGroup KellyGroup PerlmanGroup VanSnellenbergGroup CheungGroup KhosronejadGroup PernaGroup VaskaGroup ChowdhuryGroup KimGroup PicartGroup VeeramahGroup ChowdhuryRGroup KirylukGroup PiretGroup VitekGroup ColleGroup KodnerGroup PolakGroup VonDerLindenGroup CollierGroup KogaGroup PoonGroup VorkasGroup CSE416 KozakovGroup PowersGroup WangGroup CSE504 KritzerGroup PSY610 WanGroup CSE519 KrsticGroup PSY620 WangXGroup CSE590 KrsticQuantumGroup QuantComp WeinachtGroup CSE628 KurcGroup RahmeGroup WeinsteinGroup DAndreaGroup LeungGroup RajputGroup WeissmanGroup DavalosGroup LevineGroup RambowGroup WilsonGroup DeLorenzoGroup LiGroup RestGroup WymoreGroup DengYasarGroup LoverdeGroup ReuterGroup YeGroup DevarajanGroup LuGroup RiosGroup YouGroup DheillyGroup LuhmannGroup rizzo ZhangGroup DillGroup LuoGroup rjh ZhanGroup DoboliGroup LynchGroup RosatiGroup ZhangYGroup DubnauGroup MaffeiGroup samples ZhaoGroup EBH370 MaGroup SampsonCryoEMGroup ZhouGroup EBH381 MakGroup SampsonGroup ZhouMedAdvGroup EkblomGroup MallipattuGroup SamulyakGroup ZhuGroup (base) [ehspector@login2 projects]$ cd AMS536 (base) [ehspector@login2 AMS536]$ cd zzz.programs (base) [ehspector@login2 zzz.programs]$ ls amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber dock6.10 dock6.12 gen-frags-12 VS_libraries dock6.10_milan dock6.12_ams536 old (base) [ehspector@login2 zzz.programs]$ cd dock6.12_ams536/ (base) [ehspector@login2 dock6.12_ams536]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@login2 dock6.12_ams536]$ cd bin/ (base) [ehspector@login2 bin]$ ls am1bcc dock6.mpi multigrid_fp_gen.py sevsolv amberize_complex espgen nchemgrid_GB showbox amberize_ligand grid nchemgrid_SA showsphere amberize_receptor grid-convert parmcal solvgrid antechamber grid-convrds parmchk solvmap atomtype make_phimap prepare_amber.pl sphere_selector bondtype mol2bild.py prepare_rna_amber.pl sphgen chemgrid mol2.py prepgen teLeap combine_torenv.py mopac resp tleap dock6 mopac.sh respgen (base) [ehspector@login2 bin]$ cd (base) [ehspector@login2 ~]$ man date (base) [ehspector@login2 ~]$ (base) [ehspector@login2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@login2 ~]$ cd .. (base) [ehspector@login2 home]$ cd .. (base) [ehspector@login2 gpfs]$ cd projects/AMS536/ (base) [ehspector@login2 AMS536]$ ls 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 2020 2022 2024 get_anchors.py zzz.anchors (base) [ehspector@login2 AMS536]$ cd 2025/ (base) [ehspector@login2 2025]$ ls additional_files rotations (base) [ehspector@login2 2025]$ cd rotations/ (base) [ehspector@login2 rotations]$ ls aokisamen (base) [ehspector@login2 rotations]$ cd .. (base) [ehspector@login2 2025]$ cd .. (base) [ehspector@login2 AMS536]$ ls 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 2020 2022 2024 get_anchors.py zzz.anchors (base) [ehspector@login2 AMS536]$ cd 2025/ (base) [ehspector@login2 2025]$ ls additional_files rotations (base) [ehspector@login2 2025]$ cd additional_files/ (base) [ehspector@login2 additional_files]$ ls sample_bashrc_4seawulf.txt sample_slurm_submission.sh test.txt touch.sh (base) [ehspector@login2 additional_files]$ ls sample_bashrc_4seawulf.txt sample_slurm_submission.sh test.txt touch.sh (base) [ehspector@login2 additional_files]$ cd .. (base) [ehspector@login2 2025]$ ls additional_files rotations (base) [ehspector@login2 2025]$ cd .. (base) [ehspector@login2 AMS536]$ ls 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 2020 2022 2024 get_anchors.py zzz.anchors (base) [ehspector@login2 AMS536]$ vi junk.txt (base) [ehspector@login2 AMS536]$ ls 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 2020 2022 2024 get_anchors.py zzz.anchors (base) [ehspector@login2 AMS536]$ ls 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 2020 2022 2024 get_anchors.py zzz.anchors (base) [ehspector@login2 AMS536]$ cd 2025 (base) [ehspector@login2 2025]$ ls additional_files rotations wed_fun.txt (base) [ehspector@login2 2025]$ ls additional_files rotations wed_humpday.txt (base) [ehspector@login2 2025]$ cd (base) [ehspector@login2 ~]$ cd ../../ (base) [ehspector@login2 gpfs]$ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST gpu up 8:00:00 1 drain sn-nvda5 gpu up 8:00:00 5 alloc sn-nvda[3-4,6-8] p100 up 1-00:00:00 1 alloc cn-nvidia gpu-long up 2-00:00:00 1 drain sn-nvda5 gpu-long up 2-00:00:00 5 alloc sn-nvda[3-4,6-8] gpu-large up 8:00:00 1 drain sn-nvda5 gpu-large up 8:00:00 5 alloc sn-nvda[3-4,6-8] debug-28core up 1:00:00 1 boot* sn046 debug-28core up 1:00:00 6 drain* sn[030-032,107-109] debug-28core up 1:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150] debug-28core up 1:00:00 12 idle sn[003-004,025-026,043-044,151-156] extended-28core up 7-00:00:00 1 boot* sn046 extended-28core up 7-00:00:00 6 drain* sn[030-032,107-109] extended-28core up 7-00:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150] extended-28core up 7-00:00:00 12 idle sn[003-004,025-026,043-044,151-156] large-28core up 8:00:00 1 boot* sn046 large-28core up 8:00:00 6 drain* sn[030-032,107-109] large-28core up 8:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150] large-28core up 8:00:00 12 idle sn[003-004,025-026,043-044,151-156] long-28core up 2-00:00:00 1 boot* sn046 long-28core up 2-00:00:00 6 drain* sn[030-032,107-109] long-28core up 2-00:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150] long-28core up 2-00:00:00 12 idle sn[003-004,025-026,043-044,151-156] medium-28core up 12:00:00 1 boot* sn046 medium-28core up 12:00:00 6 drain* sn[030-032,107-109] medium-28core up 12:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150] medium-28core up 12:00:00 12 idle sn[003-004,025-026,043-044,151-156] short-28core up 4:00:00 1 boot* sn046 short-28core up 4:00:00 6 drain* sn[030-032,107-109] short-28core up 4:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150] short-28core up 4:00:00 12 idle sn[003-004,025-026,043-044,151-156] v100 up 1-00:00:00 2 idle sn-nvda[1-2] (base) [ehspector@login2 gpfs]$ alias alias class='cd /gpfs/home/ehspector/AMS_536' alias egrep='egrep --color=auto' alias fgrep='fgrep --color=auto' alias grep='grep --color=auto' alias home='cd /gpfs/projects/rizzo/espector' alias l.='ls -d .* --color=auto' alias ll='ls -l --color=auto' alias ls='ls --color=auto' alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash' alias vi='vim' alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde' (base) [ehspector@login2 gpfs]$ class (base) [ehspector@login2 AMS_536]$ ls class_project class_work (base) [ehspector@login2 AMS_536]$ cd class_work/ (base) [ehspector@login2 class_work]$ ls (base) [ehspector@login2 class_work]$ touch Notes.txt (base) [ehspector@login2 class_work]$ vi Notes.txt (base) [ehspector@login2 class_work]$ vi Notes.txt (base) [ehspector@login2 class_work]$ vi Notes.txt (base) [ehspector@login2 class_work]$ class (base) [ehspector@login2 AMS_536]$ cd .. (base) [ehspector@login2 ~]$ class (base) [ehspector@login2 AMS_536]$ ls class_project class_work (base) [ehspector@login2 AMS_536]$ cd class_work/ (base) [ehspector@login2 class_work]$ ls Notes.txt (base) [ehspector@login2 class_work]$ vi Notes.txt (base) [ehspector@login2 class_work]$ vi Notes.txt (base) [ehspector@login2 class_work]$ alias alias class='cd /gpfs/home/ehspector/AMS_536' alias egrep='egrep --color=auto' alias fgrep='fgrep --color=auto' alias grep='grep --color=auto' alias home='cd /gpfs/projects/rizzo/espector' alias l.='ls -d .* --color=auto' alias ll='ls -l --color=auto' alias ls='ls --color=auto' alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash' alias vi='vim' alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde' (base) [ehspector@login2 class_work]$ which dock6 /gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6 (base) [ehspector@login2 class_work]$ vi Notes.txt (base) [ehspector@login2 class_work]$ vi ~/.bashrc (base) [ehspector@login2 class_work]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP PHYS_561 % cd (base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_500 (base) supremestudier@Evans-MBP AMS_500 % ls Materials (base) supremestudier@Evans-MBP AMS_500 % mkdir Week_2 (base) supremestudier@Evans-MBP AMS_500 % which python /Users/supremestudier/anaconda3/bin/python (base) supremestudier@Evans-MBP AMS_500 % pip install polaris-lib Collecting polaris-lib

 Obtaining dependency information for polaris-lib from https://files.pythonhosted.org/packages/5f/69/3a9d76a53ebc41245755a71968e7789c543fe93cb48fff5b0a0a54aff56b/polaris_lib-0.11.6-py3-none-any.whl.metadata
 Downloading polaris_lib-0.11.6-py3-none-any.whl.metadata (5.9 kB)

Collecting authlib (from polaris-lib)

 Obtaining dependency information for authlib from https://files.pythonhosted.org/packages/e8/6a/e83a6c04f8c6014c33d97c135782a55370cf60513f8d9f99f1279c7f9c13/Authlib-1.4.1-py2.py3-none-any.whl.metadata
 Downloading Authlib-1.4.1-py2.py3-none-any.whl.metadata (3.9 kB)

Collecting boto3<1.36.0 (from polaris-lib)

 Obtaining dependency information for boto3<1.36.0 from https://files.pythonhosted.org/packages/65/77/8bbca82f70b062181cf0ae53fd43f1ac6556f3078884bfef9da2269c06a3/boto3-1.35.99-py3-none-any.whl.metadata
 Downloading boto3-1.35.99-py3-none-any.whl.metadata (6.7 kB)

Collecting datamol>=0.12.1 (from polaris-lib)

 Obtaining dependency information for datamol>=0.12.1 from https://files.pythonhosted.org/packages/d4/e7/3df58df1af04dcc694a6c970e7138ba3ec3447a442deb427914438326107/datamol-0.12.5-py3-none-any.whl.metadata
 Downloading datamol-0.12.5-py3-none-any.whl.metadata (8.0 kB)

Collecting fastpdb (from polaris-lib)

 Obtaining dependency information for fastpdb from https://files.pythonhosted.org/packages/ff/e3/be3b68743930f079776cdfa7d6475278c2160f77d2610fd4e98a1ae1c545/fastpdb-1.3.1-cp311-cp311-macosx_10_12_x86_64.whl.metadata
 Downloading fastpdb-1.3.1-cp311-cp311-macosx_10_12_x86_64.whl.metadata (1.9 kB)

Requirement already satisfied: fsspec[http] in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (2023.4.0) Collecting httpx (from polaris-lib)

 Obtaining dependency information for httpx from https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl.metadata
 Downloading httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)

Collecting numcodecs[msgpack]>=0.13.1 (from polaris-lib)

 Obtaining dependency information for numcodecs[msgpack]>=0.13.1 from https://files.pythonhosted.org/packages/55/9c/5a540965c87f1d553748114734bf808d396e629080d4432e745adee02f09/numcodecs-0.15.0-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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Requirement already satisfied: numpy<2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (1.24.3) Requirement already satisfied: pandas in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (2.0.3) Requirement already satisfied: pyarrow<18 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (11.0.0) Collecting pydantic>=2 (from polaris-lib)

 Obtaining dependency information for pydantic>=2 from https://files.pythonhosted.org/packages/f4/3c/8cc1cc84deffa6e25d2d0c688ebb80635dfdbf1dbea3e30c541c8cf4d860/pydantic-2.10.6-py3-none-any.whl.metadata
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Collecting pydantic-settings>=2 (from polaris-lib)

 Obtaining dependency information for pydantic-settings>=2 from https://files.pythonhosted.org/packages/b4/46/93416fdae86d40879714f72956ac14df9c7b76f7d41a4d68aa9f71a0028b/pydantic_settings-2.7.1-py3-none-any.whl.metadata
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Collecting pyroaring (from polaris-lib)

 Obtaining dependency information for pyroaring from https://files.pythonhosted.org/packages/88/b5/ade9df73cd73a742d9a97722234435b0860827942c9d552433a8e40f7050/pyroaring-1.0.0-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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Requirement already satisfied: pyyaml in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (6.0) Requirement already satisfied: rich>=13.9.4 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (13.9.4) Requirement already satisfied: scikit-learn in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (1.3.0) Requirement already satisfied: scipy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (1.11.1) Requirement already satisfied: seaborn in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (0.12.2) Collecting typer (from polaris-lib)

 Obtaining dependency information for typer from https://files.pythonhosted.org/packages/d0/cc/0a838ba5ca64dc832aa43f727bd586309846b0ffb2ce52422543e6075e8a/typer-0.15.1-py3-none-any.whl.metadata
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Collecting typing-extensions>=4.12.0 (from polaris-lib)

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Collecting botocore<1.36.0,>=1.35.99 (from boto3<1.36.0->polaris-lib)

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 Obtaining dependency information for s3transfer<0.11.0,>=0.10.0 from https://files.pythonhosted.org/packages/66/05/7957af15543b8c9799209506df4660cba7afc4cf94bfb60513827e96bed6/s3transfer-0.10.4-py3-none-any.whl.metadata
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 Building wheel for asciitree (setup.py) ... done
 Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5032 sha256=24fc75d0363ae85814cc0078da13ef4692220652876b36186c2bc8fd449fbede
 Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/71/c1/da/23077eb3b87d24d6f3852ed1ed1a1ac2d3c885ad6ebd2b4a07

Successfully built asciitree Installing collected packages: pyroaring, asciitree, typing-extensions, shellingham, selfies, numpy, loguru, importlib-resources, h11, fasteners, deprecated, annotated-types, scipy, rdkit, pydantic-core, numcodecs, httpcore, botocore, zarr, typer, s3transfer, pydantic, httpx, biotraj, authlib, pydantic-settings, datamol, boto3, biotite, fastpdb, polaris-lib

 Attempting uninstall: typing-extensions
   Found existing installation: typing_extensions 4.7.1
   Uninstalling typing_extensions-4.7.1:
     Successfully uninstalled typing_extensions-4.7.1
 Attempting uninstall: numpy
   Found existing installation: numpy 1.24.3
   Uninstalling numpy-1.24.3:
     Successfully uninstalled numpy-1.24.3
 Attempting uninstall: scipy
   Found existing installation: scipy 1.11.1
   Uninstalling scipy-1.11.1:
     Successfully uninstalled scipy-1.11.1
 Attempting uninstall: botocore
   Found existing installation: botocore 1.29.76
   Uninstalling botocore-1.29.76:
     Successfully uninstalled botocore-1.29.76
 Attempting uninstall: pydantic
   Found existing installation: pydantic 1.10.8
   Uninstalling pydantic-1.10.8:
     Successfully uninstalled pydantic-1.10.8

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. tables 3.8.0 requires blosc2~=2.0.0, which is not installed. tables 3.8.0 requires cython>=0.29.21, which is not installed. gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed. numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.4 which is incompatible. anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible. aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible. Successfully installed annotated-types-0.7.0 asciitree-0.3.3 authlib-1.4.1 biotite-1.1.0 biotraj-1.2.2 boto3-1.35.99 botocore-1.35.99 datamol-0.12.5 deprecated-1.2.18 fasteners-0.19 fastpdb-1.3.1 h11-0.14.0 httpcore-1.0.7 httpx-0.28.1 importlib-resources-6.5.2 loguru-0.7.3 numcodecs-0.15.0 numpy-1.26.4 polaris-lib-0.11.6 pydantic-2.10.6 pydantic-core-2.27.2 pydantic-settings-2.7.1 pyroaring-1.0.0 rdkit-2024.9.4 s3transfer-0.10.4 scipy-1.15.1 selfies-2.2.0 shellingham-1.5.4 typer-0.15.1 typing-extensions-4.12.2 zarr-2.18.4 (base) supremestudier@Evans-MBP AMS_500 % polaris login [2025-01-31 19:47:50] INFO Your browser has been opened to visit: external_client.py:149

                              https://clerk.polarishub.io/oauth/auth                       
                              orize?response_type=code&client_id=agQ                       
                              P2xVM6JqMHvGc&redirect_uri=https%3A%2F                       
                              %2Fpolarishub.io%2Foauth2%2Fcallback&s                       
                              cope=profile+email&state=YEjoNaFiIPI4k                       
                              rv6quFJFVgB09TcYM&code_challenge=QG1cf                       
                              HPgkiyqBUkzPRKUxet5FXo5xZWG21Lh_QXjhSU                       
                              &code_challenge_method=S256

Please enter the authorization token: 013927 ╭─────────────────────────── Traceback (most recent call last) ────────────────────────────╮ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/cli.py:31 in login │ │ │ │ 28 │ This CLI will use the OAuth2 protocol to gain token-based access to the Polaris │ │ 29 │ """ │ │ 30 │ client = PolarisHubClient(settings=PolarisHubSettings(_env_file=client_env_file │ │ ❱ 31 │ client.login(auto_open_browser=auto_open_browser, overwrite=overwrite) │ │ 32 │ │ 33 │ │ 34 @app.command(hidden=True) │ │ │ │ ╭──────────────────────────────────── locals ─────────────────────────────────────╮ │ │ │ auto_open_browser = True │ │ │ │ client = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │ │ │ │ client_env_file = '.env' │ │ │ │ overwrite = False │ │ │ ╰─────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/client.py:249 │ │ in login │ │ │ │ 246 │ │ │ auto_open_browser: Whether to automatically open the browser to visit │ │ 247 │ │ """ │ │ 248 │ │ if overwrite or self.token is None or not self.ensure_active_token(): │ │ ❱ 249 │ │ │ self.external_client.interactive_login(overwrite=overwrite, auto_open_ │ │ 250 │ │ │ self.token = self.fetch_token() │ │ 251 │ │ │ │ 252 │ │ logger.info("You are successfully logged in to the Polaris Hub.") │ │ │ │ ╭──────────────────────────────────── locals ─────────────────────────────────────╮ │ │ │ auto_open_browser = True │ │ │ │ overwrite = False │ │ │ │ self = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │ │ │ ╰─────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │ │ .py:158 in interactive_login │ │ │ │ 155 │ │ authorization_code = input("Please enter the authorization token: ") │ │ 156 │ │ │ │ 157 │ │ # Step 3: Exchange authorization code for an access token │ │ ❱ 158 │ │ self.fetch_token(code=authorization_code, grant_type="authorization_code") │ │ 159 │ │ │ │ 160 │ │ logger.info(f"Successfully authenticated to the Polaris Hub as `{self.user │ │ 161 │ │ │ │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │ │ │ _ = 'YEjoNaFiIPI4krv6quFJFVgB09TcYM' │ │ │ │ authorization_code = '013927' │ │ │ │ authorization_url = 'https://clerk.polarishub.io/oauth/authorize?response_type=cod… │ │ │ │ auto_open_browser = True │ │ │ │ overwrite = False │ │ │ │ self = <polaris.hub.external_client.ExternalAuthClient object at │ │ │ │ 0x1356cad90> │ │ │ │ token_is_valid = False │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │ │ .py:74 in fetch_token │ │ │ │ 71 │ def fetch_token(self, **kwargs) -> dict: │ │ 72 │ │ """Light wrapper to automatically pass in the right URL""" │ │ 73 │ │ try: │ │ ❱ 74 │ │ │ return super().fetch_token( │ │ 75 │ │ │ │ url=self.settings.token_fetch_url, code_verifier=self.code_verifie │ │ 76 │ │ │ ) │ │ 77 │ │ except OAuth2Error as error: │ │ │ │ ╭──────────────────────────────────── locals ─────────────────────────────────────╮ │ │ │ kwargs = {'code': '013927', 'grant_type': 'authorization_code'} │ │ │ │ self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │ │ │ ╰─────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:21 │ │ 7 in fetch_token │ │ │ │ 214 │ │ if url is None: │ │ 215 │ │ │ url = self.metadata.get('token_endpoint') │ │ 216 │ │ │ │ ❱ 217 │ │ return self._fetch_token( │ │ 218 │ │ │ url, body=body, auth=auth, method=method, │ │ 219 │ │ │ headers=headers, **session_kwargs │ │ 220 │ │ ) │ │ │ │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │ │ │ auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2Cli… │ │ │ │ object at 0x136f50190> │ │ │ │ authorization_response = None │ │ │ │ body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2F… │ │ │ │ grant_type = 'authorization_code' │ │ │ │ headers = { │ │ │ │ │ 'Accept': 'application/json', │ │ │ │ │ 'Content-Type': │ │ │ │ 'application/x-www-form-urlencoded;charset=UTF-8' │ │ │ │ } │ │ │ │ kwargs = { │ │ │ │ │ 'code_verifier': │ │ │ │ 'S2qmBfN72W2onFO2So06MzNLUB8yVXmHmp4m9xisHaIUA9zU', │ │ │ │ │ 'code': '013927' │ │ │ │ } │ │ │ │ method = 'POST' │ │ │ │ self = <polaris.hub.external_client.ExternalAuthClient object at │ │ │ │ 0x1356cad90> │ │ │ │ session_kwargs = {} │ │ │ │ state = None │ │ │ │ url = 'https://clerk.polarishub.io/oauth/token' │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:37 │ │ 9 in _fetch_token │ │ │ │ 376 │ │ for hook in self.compliance_hook['access_token_response']: │ │ 377 │ │ │ resp = hook(resp) │ │ 378 │ │ │ │ ❱ 379 │ │ return self.parse_response_token(resp) │ │ 380 │ │ │ 381 │ def _refresh_token(self, url, refresh_token=None, body=, headers=None, │ │ 382 │ │ │ │ │ auth=None, **kwargs): │ │ │ │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │ │ │ auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2ClientAuth object │ │ │ │ at 0x136f50190> │ │ │ │ body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2Fpolarishub.io%2… │ │ │ │ headers = { │ │ │ │ │ 'Accept': 'application/json', │ │ │ │ │ 'Content-Type': 'application/x-www-form-urlencoded;charset=UTF-8' │ │ │ │ } │ │ │ │ kwargs = {} │ │ │ │ method = 'POST' │ │ │ │ resp = <Response [401 Unauthorized]> │ │ │ │ self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │ │ │ │ url = 'https://clerk.polarishub.io/oauth/token' │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:35 │ │ 5 in parse_response_token │ │ │ │ 352 │ │ │ │ 353 │ │ token = resp.json() │ │ 354 │ │ if 'error' in token: │ │ ❱ 355 │ │ │ raise self.oauth_error_class( │ │ 356 │ │ │ │ error=token['error'], │ │ 357 │ │ │ │ description=token.get('error_description') │ │ 358 │ │ │ ) │ │ │ │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │ │ │ resp = <Response [401 Unauthorized]> │ │ │ │ self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │ │ │ │ token = { │ │ │ │ │ 'error': 'invalid_grant', │ │ │ │ │ 'error_description': 'The provided authorization grant (e.g., │ │ │ │ authorization code, resource owner crede'+156 │ │ │ │ } │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────────────────╯ OAuthError: invalid_grant: The provided authorization grant (e.g., authorization code, resource owner credentials) or refresh token is invalid, expired, revoked, does not match the redirection URI used in the authorization request, or was issued to another client (base) supremestudier@Evans-MBP AMS_500 % polaris login [2025-01-31 19:49:32] INFO Your browser has been opened to visit: external_client.py:149

                              https://clerk.polarishub.io/oauth/auth                       
                              orize?response_type=code&client_id=agQ                       
                              P2xVM6JqMHvGc&redirect_uri=https%3A%2F                       
                              %2Fpolarishub.io%2Foauth2%2Fcallback&s                       
                              cope=profile+email&state=qo1ea4ucZsaZS                       
                              OGFfAWK47Skq0G4jU&code_challenge=irfzd                       
                              YmRLZliQeiwg2GQYa156QMYqb4zXHNXQJFb0pE                       
                              &code_challenge_method=S256

Please enter the authorization token: MTLLNZK2ZWETMDBMMY0ZMGU5LWJJYZKTZWI5MZYWMDHIOTCZ [2025-01-31 19:49:45] INFO Successfully authenticated to the external_client.py:160

                              Polaris Hub as                                               
                              `evan.spector@stonybrook.edu`! 🎉

[2025-01-31 19:49:46] INFO You are successfully logged in to the Polaris client.py:252

                              Hub.

(base) supremestudier@Evans-MBP AMS_500 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: (base) [ehspector@login1 ~]$ home (base) [ehspector@login1 espector]$ module list Currently Loaded Modulefiles:

1) slurm/17.11.12   2) shared   3) gcc/13.2.0   4) mvapich2/gcc13.2/2.3.7   5) gcc-stack

(base) [ehspector@login1 espector]$ module load git WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.

/cm/local/apps/environment-modules/4.0.0//bin

(base) [ehspector@login1 espector]$ git diff warning: Not a git repository. Use --no-index to compare two paths outside a working tree usage: git diff --no-index [<options>] <path> <path>

Diff output format options

   -p, --patch           generate patch
   -s, --no-patch        suppress diff output
   -u                    generate patch
   -U, --unified[=<n>]   generate diffs with <n> lines context
   -W, --function-context
                         generate diffs with <n> lines context
   --raw                 generate the diff in raw format
   --patch-with-raw      synonym for '-p --raw'
   --patch-with-stat     synonym for '-p --stat'
   --numstat             machine friendly --stat
   --shortstat           output only the last line of --stat
   -X, --dirstat[=<param1,param2>...]
                         output the distribution of relative amount of changes for each sub-directory
   --cumulative          synonym for --dirstat=cumulative
   --dirstat-by-file[=<param1,param2>...]
                         synonym for --dirstat=files,param1,param2...
   --check               warn if changes introduce conflict markers or whitespace errors
   --summary             condensed summary such as creations, renames and mode changes
   --name-only           show only names of changed files
   --name-status         show only names and status of changed files
   --stat[=<width>[,<name-width>[,<count>]]]
                         generate diffstat
   --stat-width <width>  generate diffstat with a given width
   --stat-name-width <width>
                         generate diffstat with a given name width
   --stat-graph-width <width>
                         generate diffstat with a given graph width
   --stat-count <count>  generate diffstat with limited lines
   --compact-summary     generate compact summary in diffstat
   --binary              output a binary diff that can be applied
   --full-index          show full pre- and post-image object names on the "index" lines
   --color[=<when>]      show colored diff
   --ws-error-highlight <kind>
                         highlight whitespace errors in the 'context', 'old' or 'new' lines in the diff
   -z                    do not munge pathnames and use NULs as output field terminators in --raw or --numstat
   --abbrev[=<n>]        use <n> digits to display object names
   --src-prefix <prefix>
                         show the given source prefix instead of "a/"
   --dst-prefix <prefix>
                         show the given destination prefix instead of "b/"
   --line-prefix <prefix>
                         prepend an additional prefix to every line of output
   --no-prefix           do not show any source or destination prefix
   --inter-hunk-context <n>
                         show context between diff hunks up to the specified number of lines
   --output-indicator-new <char>
                         specify the character to indicate a new line instead of '+'
   --output-indicator-old <char>
                         specify the character to indicate an old line instead of '-'
   --output-indicator-context <char>
                         specify the character to indicate a context instead of ' '

Diff rename options

   -B, --break-rewrites[=<n>[/<m>]]
                         break complete rewrite changes into pairs of delete and create
   -M, --find-renames[=<n>]
                         detect renames
   -D, --irreversible-delete
                         omit the preimage for deletes
   -C, --find-copies[=<n>]
                         detect copies
   --find-copies-harder  use unmodified files as source to find copies
   --no-renames          disable rename detection
   --rename-empty        use empty blobs as rename source
   --follow              continue listing the history of a file beyond renames
   -l <n>                prevent rename/copy detection if the number of rename/copy targets exceeds given limit

Diff algorithm options

   --minimal             produce the smallest possible diff
   -w, --ignore-all-space
                         ignore whitespace when comparing lines
   -b, --ignore-space-change
                         ignore changes in amount of whitespace
   --ignore-space-at-eol
                         ignore changes in whitespace at EOL
   --ignore-cr-at-eol    ignore carrier-return at the end of line
   --ignore-blank-lines  ignore changes whose lines are all blank
   -I, --ignore-matching-lines <regex>
                         ignore changes whose all lines match <regex>
   --indent-heuristic    heuristic to shift diff hunk boundaries for easy reading
   --patience            generate diff using the "patience diff" algorithm
   --histogram           generate diff using the "histogram diff" algorithm
   --diff-algorithm <algorithm>
                         choose a diff algorithm
   --anchored <text>     generate diff using the "anchored diff" algorithm
   --word-diff[=<mode>]  show word diff, using <mode> to delimit changed words
   --word-diff-regex <regex>
                         use <regex> to decide what a word is
   --color-words[=<regex>]
                         equivalent to --word-diff=color --word-diff-regex=<regex>
   --color-moved[=<mode>]
                         moved lines of code are colored differently
   --color-moved-ws <mode>
                         how white spaces are ignored in --color-moved

Other diff options

   --relative[=<prefix>]
                         when run from subdir, exclude changes outside and show relative paths
   -a, --text            treat all files as text
   -R                    swap two inputs, reverse the diff
   --exit-code           exit with 1 if there were differences, 0 otherwise
   --quiet               disable all output of the program
   --ext-diff            allow an external diff helper to be executed
   --textconv            run external text conversion filters when comparing binary files
   --ignore-submodules[=<when>]
                         ignore changes to submodules in the diff generation
   --submodule[=<format>]
                         specify how differences in submodules are shown
   --ita-invisible-in-index
                         hide 'git add -N' entries from the index
   --ita-visible-in-index
                         treat 'git add -N' entries as real in the index
   -S <string>           look for differences that change the number of occurrences of the specified string
   -G <regex>            look for differences that change the number of occurrences of the specified regex
   --pickaxe-all         show all changes in the changeset with -S or -G
   --pickaxe-regex       treat <string> in -S as extended POSIX regular expression
   -O <file>             control the order in which files appear in the output
   --rotate-to <path>    show the change in the specified path first
   --skip-to <path>      skip the output to the specified path
   --find-object <object-id>
                         look for differences that change the number of occurrences of the specified object
   --diff-filter [(A|C|D|M|R|T|U|X|B)...[*]]
                         select files by diff type
   --output <file>       output to a specific file

(base) [ehspector@login1 espector]$ git status fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). (base) [ehspector@login1 espector]$ git branch fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ module list Currently Loaded Modulefiles:

1) slurm/17.11.12   3) gcc/13.2.0               5) gcc-stack   
2) shared           4) mvapich2/gcc13.2/2.3.7   6) git/2.36.2

(base) [ehspector@login1 espector]$ history

   9  make rdkit
  10  modue list
  11  module list
  12  module unload gcc
  13  module list
  14  module unload mvapich2/gcc13.2/2.3.7 
  15  module unload gcc-stack
  16  module list
  17  module load gcc/7.2.0 
  18  which gcc
  19  make rdkitclean
  20  make rdkit
  21  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
  22  vi ~/.bashrc
  23  module list
  24  ls
  25  source ~/.bashrc
  26  module list
  27  ls
  28  vi ~/.bashrc
  29  make clean
  30  ./configure gnu.rdkit
  31  make dock
  32  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
  33  home
  34  cd RDKit/gas/
  35  ls
  36  sbatch 4s0v_filter.slurm 
  37  vi 4s0v_filter.slurm 
  38  sbatch 4s0v_filter.slurm 
  39  squeue -u ehspector
  40  vi 4s0v_filter.slurm 
  41  squeue -u ehspector
  42  cd ..
  43  cd 4s0v/
  44  cd GA
  45  ls
  46  cd 4s0v_GA_results/
  47  ls
  48  vi 4s0v_GA_output.restart0000.mol2 
  49  vi 4s0v_GA_output.restart0001.mol2 
  50  cd ..
  51  ls
  52  cd virtual_screening/
  53  ls
  54  vi virtual.in 
  55  squeue -u ehspector
  56  cd ..
  57  cd RDKit/gas/
  58  ls
  59  vi filter_out.txt 
  60  cd ..
  61  cd 4s0v/gas_teiger/
  62  ls
  63  touch gas_rdkit
  64  dock6 -i gas_rdkit 
  65  which dock
  66  vi ~/.bashrc
  67  source ~/.bashrc
  68  which dock
  69  which rdkit
  70  source ~/.bashrc
  71  which dock6
  72  which dock6.rdkit
  73  vi ~/.bashrc
  74  source ~/.bashrc
  75  which dock6.rdkit
  76  ls
  77  dock6.rdkit -i gas_rdkit 
  78  rm gas_rdkit 
  79  cd ..
  80  cd RDKit/
  81  cd gas
  82  sbatch 4s0v_filter.slurm 
  83  squeue -u ehspector
  84  ls
  85  squeue -u ehspector
  86  ls
  87  vi output_scored.mol2 
  88  squeue -u ehspector
  89  vi output_scored.mol2 
  90  cd ..
  91  vi output_scored.mol2 
  92  cd ..
  93  cd 4s0v/
  94  ls
  95  cd GA_data/
  96  ls
  97  cd ..
  98  cd GA
  99  ls
 100  cd ..
 101  cd gas_teiger/
 102  ls
 103  touch gas_rd.in
 104  dock6.rdkit gas_rd.in 
 105  cd ..
 106  cd gas_teiger/
 107  dock6 -i gas_rd.in 
 108  rm gas_rd.in 
 109  cd ..
 110  ls
 111  cd ..
 112  cd builds/alpha_branch/src/dock
 113  vi filter.cpp
 114  cd ..
 115  cd install/
 116  make clean
 117  make dock
 118  ls
 119  ./configure
 120  ./configure gnu
 121  make -i distclean
 122  make dock
 123  ./configure
 124  ./configure gnu
 125  make clean
 126  ./configure gnu
 127  make dock
 128  module unload gcc/7.2.0 
 129  module load gcc-stack 
 130  make dock
 131  cd ..
 132  cd ../..
 133  ls
 134  cd 4s0v/gas_teiger/
 135  ls
 136  dock6 -i  gas.in
 137  ls
 138  vi gas.out_scored.mol2 
 139  cd ..
 140  cd builds/alpha_branch/src/dock
 141  ls
 142  vi filter.cpp 
 143  cd ../..
 144  cd install/
 145  make clean
 146  make dock
 147  cd ../../..
 148  cd 4s0v/gas_teiger/
 149  dock6 -i gas.in 
 150  ls
 151  vi gas.out_scored.mol2 
 152  cd ../..
 153  cd builds/alpha_branch/src/dock
 154  vi filter.cpp 
 155  cd ..]
 156  cd ..
 157  cd install/
 158  make clean
 159  make dock
 160  make clean
 161  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
 162  home
 163  module list
 164  cd 4s0v/
 165  ls
 166  cd GA
 167  ls
 168  squeue -u ehspector
 169  ls
 170  cd 4s0v_GA_results/
 171  ls
 172  cd ..
 173  ls
 174  cd gas_test/
 175  ls
 176  vi test.in 
 177  dock6 -i test.in
 178  ls
 179  vi test.in 
 180  dock6 -i test.in 
 181  cd ..
 182  cp 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/
 183  ls
 184  cd gas_test/
 185  ls
 186  mkdir gas_f_test 
 187  ls
 188  cd ..
 189  cp 4s0v/GA/4s0v_GA_results/4s0v_GA.slurm gas_test/gas_f_test/
 190  cd gas_test/
 191  mv gas_f_test/4s0v_GA.slurm gas_test
 192  ls
 193  cd gas_f_test/
 194  ls
 195  cd ..
 196  mv gas_test 4s0v_GA.slurm
 197  ls
 198  vi 4s0v_GA.slurm 
 199  vi 4s0v_GA.in 
 200  cd ..
 201  cd 4s0v/GA
 202  ls
 203  cd 4s0v_fraglib/
 204  pwd
 205  cd ..
 206  cd gas_test/
 207  ls
 208  vi 4s0v_GA.in 
 209  cd ..
 210  ls
 211  cd ..
 212  ls
 213  cd zzz.programs/
 214  ls
 215  cd ..
 216  cd espector/
 217  ls
 218  cd gas_test/
 219  ls
 220  vi 4s0v_GA.in 
 221  vi 4s0v_GA.slurm 
 222  vi 4s0v_GA.
 223  vi 4s0v_GA.in 
 224  vi 4s0v_GA.slurm 
 225  sbatch 4s0v_GA.slurm 
 226  squeue -u ehspector
 227  exit
 228  squeue -u ehspector
 229  exit
 230  home
 231  squeue -u ehspector
 232  exir
 233  exit
 234  home
 235  squeue -u ehspector
 236  ls
 237  cd gas_test/
 238  ls
 239  cd gas_f_test/
 240  ls
 241  cd ..
 242  vi GA.txt 
 243  cd ..
 244  ls
 245  cd gas_test/
 246  ls
 247  vi 4s0v_GA.in 
 248  cd ..
 249  cd 4s0v/GA
 250  ls
 251  cd 4s0v_
 252  cd 4s0v_fraglib/
 253  ls
 254  cd ..
 255  ls
 256  cd 4s0v_GA_results/
 257  ls
 258  vi 4s0v_GA.in 
 259  cd ..
 260  cd 4s0v_fraglib/
 261  ls
 262  cd ..
 263  ls
 264  cd ..
 265  cd gas_test/
 266  ls
 267  vi 4s0v_GA.in 
 268  sbatch 4s0v_GA.slurm 
 269  squeue -u ehspector
 270  home
 271  cd gas_test/
 272  ls
 273  vi GA.txt 
 274  vi 4s0v_GA.in 
 275  cd ..
 276  vimdiff 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/4s0v_GA.in 
 277  cd gas_test/
 278  vi 4s0v_GA.in 
 279  sbatch 4s0v_GA.slurm 
 280  squeue -u ehspector
 281  ls
 282  vi GA.txt 
 283  vi 4s0v_GA.in 
 284  vi GA.txt 
 285  module list
 286  cd ..
 287  cd builds/
 288  cd alpha_branch/src/dock
 289  make clean
 290  make dock
 291  home
 292  ls
 293  cd RDKit/
 294  ls
 295  vi filter.in 
 296  cd 
 297  home
 298  ls
 299  cd RDKit/
 300  ls
 301  vi output_scored.mol2 
 302  cd gas/
 303  ls
 304  vi filter.in 
 305  cd gas_test/
 306  ls
 307  vi filter.in 
 308  vi output_scored.mol2 
 309  cd ..
 310  home
 311  ls
 312  cd builds/alpha_branch/src/h
 313  cd builds/alpha_branch/src/dock
 314  cd ..
 315  cd install
 316  history
 317  cd ..
 318  cd install/
 319  ./configure gnu
 320  make clean
 321  make dock
 322  cd ..
 323  ls
 324  cd ..
 325  ls
 326  cd gas_test/
 327  ls
 328  vi 4s0v_GA.in 
 329  vi 4s0v_GA.slurm 
 330  sbatch 4s0v_GA.slurm 
 331  squeue -u ehspector
 332  ls
 333  vi GA.txt \
 334  vi GA.txt 
 335  exit
 336  home
 337  ls
 338  cd RDKit/
 339  ls
 340  cd gas/
 341  ls
 342  cd ..
 343  cd gas_test/
 344  ls
 345  sbatch 4s0v_GA.slurm 
 346  vi 4s0v_GA.slurm 
 347  sbatch 4s0v_GA.slurm 
 348  squeue -u ehspector
 349  ls
 350  vi GA.txt 
 351  home
 352  cd builds/alpha_branch/install/
 353  make clean
 354  ./configure gnu
 355  cd ./install
 356  make dock
 357  cd ..
 358  module list
 359  module load gcc-stack
 360  module list
 361  cd ..
 362  ls
 363  cd gas_test/
 364  ls
 365  sbatch 4s0v_GA.slurm 
 366  squeue -u ehspector
 367  ls
 368  vi 4s0v_GA_output.restart0000.mol2 
 369  ls
 370  module list
 371  ls
 372  squeue -u ehspector
 373  ls
 374  squeue -u ehspector
 375  exit
 376  home
 377  ls
 378  cd gas_test/
 379  ls
 380  cd ..
 381  cp 4s0v/gas_teiger/gas.in gas_test/gas_f_test/
 382  cd gas_test/gas_f_test/
 383  ls
 384  vi gas.in 
 385  cd ..
 386  pwd
 387  cd gas_f_test/
 388  vi gas.in 
 389  dock6 -i gas.in -o gas_0.out
 390  ls
 391  vi gas.out_scored.mol2 
 392  vi gas_0.out 
 393  vi gas.in
 394  dock6 -i gas.in -o gas_0.out
 395  ls
 396  vi gas.out_scored.mol2 
 397  cd ..
 398  vimdiff 4s0v_GA_output.restart0000.mol2 gas_f_test/gas.out_scored.mol2 
 399  cd ..
 400  cd gas_test/
 401  vi 4s0v_GA_output.restart0000.mol2 
 402  cd gas_f_test/
 403  ls
 404  mv gas.out_scored.mol2 gas_0.out_scored.mol2
 405  ls
 406  vi gas.in 
 407  mv gas.in gas_1.in 
 408  dock6 -i gas_1.in -o gas_1.out
 409  ls
 410  mv gas.out_scored.mol2 gas_1.out_scored.mol2
 411  vi gas_1.out_scored.mol2 
 412  cd ..
 413  vi 4s0v_GA_output.restart0001.mol2 
 414  vi 4s0v_GA_output.restart0050.mol2 
 415  cd gas_f_test/
 416  ls
 417  cp gas_1.in gas_50.out
 418  mv gas_50.out gas_50.in
 419  vi gas_50.in 
 420  dock6 -i gas_50.in -o gas_50.out
 421  ls
 422  mv gas.out_scored.mol2 gas_50.out_scored.mol2
 423  vi gas_50.out_scored.mol2 
 424  cd ..
 425  vi 4s0v_GA_output.restart0050.mol2 
 426  cd gas_f_test/
 427  vi gas_50.out_scored.mol2 
 428  cd ..
 429  mkdir gas_RD_tes
 430  mv gas_RD_tes/ gas_RD_Test/
 431  ls
 432  exit
 433  make clean
 434  make dock
 435  cd ..
 436  ls
 437  home
 438  ls
 439  cd RDKit/
 440  ls
 441  vi filter
 442  vi filter.in 
 443  cd gas
 444  ls
 445  vi filter.
 446  vi filter.in 
 447  cd ..
 448  cd RDKit/
 449  cd gas/
 450  ls
 451  cd gas_test/
 452  ls
 453  cd ..
 454  cp RDKit/gas/filter.in gas_test/gas_RD_Test/
 455  cd RDKit/
 456  ls
 457  vi 4s0v_filter.slurm 
 458  cd ..
 459  home
 460  cd gas_test/
 461  ls
 462  cd gas_RD_Test/
 463  ls
 464  cd ..
 465  cd gas_RD_Test/
 466  ls
 467  cd ..
 468  cd gas_f_test/
 469  ls
 470  vi gas_0.in
 471  vi gas_1.in
 472  cd ..
 473  cd gas_RD_Test/
 474  vi filter.in 
 475  mv filter.in gas.in 
 476  dock6.rdkit -i gas.in -o gas.out 
 477  ls
 478  vi output_scored.mol2 
 479  ls
 480  vi gas.out 
 481  vi gas.in 
 482  dock6.rdkit -i gas.in -o gas.out 
 483  ls
 484  vi gas.out 
 485  vi gas.in 
 486  exit
 487  home
 488  cd builds/alpha_branch/install/
 489  make clean
 490  ls
 491  ./configure gnu.rdkit
 492  make dock
 493  module list
 494  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
 495  exit
 496  dock6.rdkit -i gas_50.in -o gas_50.out 
 497  ls
 498  grep -wc MOLECULE *.mol2
 499  diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2 
 500  diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
 501  vi diff.out 
 502  vi output_scored.mol2 
 503  cd ..
 504  cd gas_f_test/
 505  ls
 506  grep -wc MOLECULE gas_50.out_scored.mol2 
 507  diff gas_50.out_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
 508  vi diff.out 
 509  home
 510  vi ~/.bashrc
 511  source ~/.bashrc
 512  exit
 513  home
 514  cd gas_test/
 515  ls
 516  cd gas_RD_Test/
 517  ls
 518  vi gas.out 
 519  vi output_scored.mol2 
 520  vi gas.in 
 521  vi output_scored.mol2 
 522  ls
 523  cd ..
 524  ls
 525  grep -wc MOLECULE 4s0v_GA_output.restart0001.mol2 
 526  cd ..
 527  ls
 528  cd gas_test/
 529  ls
 530  cd gas_RD_Test/
 531  ls
 532  vi gas.out 
 533  vi output_rejected.mol2 
 534  cd ..
 535  vimdiff 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2 
 536  diff 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2 
 537  diff -y 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2 
 538  cd gas_RD_Test/
 539  ls
 540  cp gas.in gas_50.in
 541  vi gas_50.in 
 542  dock6.rdkit -i gas_50.in -o gas_50.out
 543  dock6.rdkit -i gas.in -o gas.out 
 544  module list
 545  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
 546  rd
 547  vi ~/.bashrc
 548  source ~/.bashrc
 549  rd
 550  home
 551  ls
 552  cd gas_test/
 553  ls
 554  cd gas_f_test/
 555  vi diff.out 
 556  cd ..
 557  cd gas_RD_test
 558  ls
 559  cd gas_RD_Test/
 560  ls
 561  vi diff.out 
 562  history
 563  ls
 564  vi output_scored.mol2 
 565  cd ..
 566  cd gas_f_test/
 567  ls
 568  vi gas_50.out_scored.mol2 
 569  home
 570  ls
 571  cd builds/
 572  ls
 573  cd ..
 574  ls
 575  cd gas_test/gas_f_test/
 576  ls
 577  vi gas_50.out_scored.mol2 
 578  awk '{print $9}' gas_50.out_scored.mol2 
 579  :q
 580  vi gas_50.out_scored.mol2 
 581  awk '{print $9}' gas_50.out_scored.mol2 
 582  :q
 583  awk '{print $9}' gas_50.out_scored.mol2 > charges.txt
 584  vi charges.txt 
 585  cd ..
 586  cd gas_RD_Test/
 587  ls
 588  awk '{print $9}' output_scored.mol2 > RD_charges.txt
 589  vi RD_charges.txt 
 590  ls
 591  cd ..
 592  ls
 593  awk '{print $9}' 4s0v_GA_output.restart0050.mol2 > charges.txt
 594  vi charges.txt 
 595  mkdir charge_data.txt
 596  ls
 597  mv charge_data.txt/ charge_data/
 598  ls
 599  mv charges.txt charge_data/
 600  cd charge_data/
 601  ls
 602  mv charges.txt original_charges.txt
 603  cd ..
 604  ls
 605  cd gas_f_test/
 606  ls
 607  mv charges.txt f_charges.txt
 608  cd ..
 609  mv gas_f_test/f_charges.txt charge_data/
 610  ls
 611  ls charge_data/
 612  ls
 613  cd gas_RD_Test/
 614  ls
 615  cd ..
 616  mv gas_RD_Test/RD_charges.txt charge_data/
 617  ls
 618  exit
 619  home 
 620  cd gas_test/
 621  cd charge_data/
 622  paste -d "," original_charges.txt f_charges.txt RD_charges.txt > gasteiger_charges.csv
 623  vi gasteiger_charges.csv
 624  vi original_charges.txt 
 625  cd ..
 626  vi 4s0v_GA_output.restart0050.mol2 
 627  ls
 628  cd charge_data/
 629  ls
 630  pwd
 631  exit
 632  home
 633  cd ..
 634  ls
 635  cd AMS536
 636  ls
 637  cd 2025
 638  ls
 639  cd additional_files/
 640  ls
 641  cd ..
 642  cd 2025
 643  pwd
 644  vi ~/.bashrc
 645  home
 646  source ~/.bashrc
 647  class
 648  home
 649  ls
 650  exit
 651  home
 652  ls
 653  cd 4s0v/
 654  ls
 655  cd gas_teiger/
 656  ls
 657  cd no_charge/
 658  ls
 659  cd ..
 660  vi no_gas.in 
 661  vi no_gas.out_scored.mol2 
 662  cd ..
 663  ls
 664  cd GA_data/
 665  ls
 666  cd ..
 667  cd gas_teiger/
 668  ls
 669  vi gas.out_scored.mol2 
 670  exit
 671  home
 672  ls
 673  cd gas_test/
 674  ls
 675  cd ..
 676  ls
 677  cd 4s0v/
 678  ls
 679  cd s
 680  cd structure/
 681  ls
 682  cd ..
 683  ls
 684  cd ..
 685  cd gas_test/
 686  ls
 687  cd gas_f_test/
 688  ls
 689  vi gas_1.in 
 690  cd ..
 691  ls
 692  cd ..
 693  cd 4s0v/gas_teiger/
 694  ls
 695  vi gas.in 
 696  module
 697  module list
 698  ls
 699  cd ..
 700  ls
 701  cd structure/
 702  ls
 703  cd ..
 704  cd gas_teiger/
 705  ls
 706  vi gas.in 
 707  dock6 -i gas.in -o gas.out
 708  ls
 709  vi gas.out
 710  vi gas.out_scored.mol2 
 711  cd ..
 712  ls
 713  vi gas_teiger/
 714  cd gas_teiger/
 715  ls
 716  vi gas.in 
 717  dock6 -i gas.in -o gas.out
 718  ls
 719  vi gas.out
 720  vi gas.out_scored.mol2 
 721  cd ..
 722  ls
 723  cd energy_min/
 724  ls
 725  cd ..
 726  ls
 727  cd 4s0v/
 728  ls
 729  vi gas_teiger/
 730  cd gas_teiger/
 731  vi gas.
 732  vi gas.in 
 733  dock6 -i gas.in -o gas.out
 734  ls
 735  vi gas.out
 736  vi gas.in
 737  cd ..
 738  cd surface_spheres/
 739  ls
 740  cd ..
 741  cd gas_test/
 742  ls
 743  cd ..
 744  ls
 745  cd 4s0v/
 746  ls
 747  cd surface_spheres/
 748  ls
 749  cd ..
 750  ls
 751  cd gas_teiger/
 752  ls
 753  vi gas.in 
 754  dock6 -i gas.in -o gas.out
 755  ls
 756  vi gas.out
 757  vi gas.out_scored.mol2 
 758  vi gas.in 
 759  dock6 -i gas.in -o gas.out
 760  ls
 761  vi gas.out
 762  vi gas.out_scored.mol2 
 763  exit
 764  home
 765  class
 766  ls
 767  cd additional_files/
 768  ls
 769  vi sample_bashrc_4seawulf.txt 
 770  exit
 771  home
 772  ls
 773  cd builds/
 774  cd alpha_branch/
 775  ls
 776  cd install/
 777  ls
 778  cd ..
 779  l
 780  ls
 781  cd install/
 782  ls
 783  cd ..
 784  ls
 785  cd bin/
 786  ls
 787  vi dock6.rdkit 
 788  cd ..
 789  cd src/
 790  ls
 791  vi Makefile 
 792  cd rdkit/
 793  ls
 794  vi Makefile 
 795  ls
 796  module list
 797  module load git
 798  module list
 799  git branch
 800  exit
 801  home
 802  ls
 803  cd gas_test/
 804  ls
 805  cd ..
 806  ls
 807  cd 4s0v/
 808  ls
 809  cd structure/
 810  ls
 811  cd ..
 812  cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
 813  cd gas_teiger/
 814  ls
 815  vi 4s0v_ligand_hydrogens_charges.mol2 
 816  pwd
 817  ls
 818  cd no_charge/
 819  ls
 820  vi gas_2.out 
 821  vi gas_2.in 
 822  cd ..
 823  mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
 824  cd no_charge/
 825  ls
 826  vi gas_2.in 
 827  dock6 -i gas_2.in -o gas_2.out
 828  vi gas_2.out
 829  vi gas_2.in 
 830  dock6 -i gas_2.in -o gas_2.out
 831  ls
 832  vi gas_2.out 
 833  vi gas_2.in 
 834  dock6 -i gas_2.in -o gas_2.out
 835  ls
 836  vi gas_2.out 
 837  mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
 838  ls
 839  cd ..
 840  cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
 841  ls
 842  cd gas_teiger/no_charge/
 843  ls
 844  vi 4s0v.lig.min_scored.mol2 
 845  vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2 
 846  vi 4s0v.lig.min_scored.mol2 
 847  mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
 848  vi gas_2.in
 849  dock6 -i gas_2.in -o gas_2.out
 850  ls
 851  vi gas_2.out 
 852  vi gas_2.in 
 853  vi gas.out_scored.mol2 
 854  exit
 855  home 
 856  cd 4s0v/
 857  ls
 858  cd gas_teiger/no_charge/
 859  vi gas_2.in 
 860  vi 4s0v.lig_no_charge.min_scored.mol2 
 861  vi gas_2.out 
 862  cd ..
 863  ls
 864  vi gas.in 
 865  vi gas.out
 866  exit
 867  home
 868  ls
 869  cd 4s0v/
 870  ls
 871  cd gas_teiger/
 872  ls
 873  vi no_gas.in 
 874  vi no_gas.out
 875  vi no_gas.out_scored.mol2 
 876  exit
 877  class
 878  pwd
 879  cd ..
 880  vi ~/.bashrc
 881  source ~/.bashrc
 882  home
 883  class
 884  exit
 885  class
 886  mkdir ehspector
 887  ls
 888  cd ehspector/
 889  ls
 890  touch file.txt
 891  ls
 892  cd ..
 893  cd
 894  ls
 895  mkdir class_project
 896  ls
 897  exit
 898  home
 899  ls
 900  cd builds/
 901  ls
 902  cd alpha_branch/
 903  ls
 904  module load git
 905  git branch
 906  git config --get remote.origin.url
 907  git pull
 908  git status
 909  git diff src/dock/dock.cpp
 910  git diff src/dock/gasteiger.cpp
 911  git diff src/dock/orient.cpp
 912  git diff src/dock/sphere.cpp
 913  ls
 914  cd src/dock
 915  vi gasteiger.cpp 
 916  git diff gasteiger.cpp 
 917  vi gasteiger.cpp 
 918  git diff gasteiger.cpp 
 919  git status gasteiger.cpp 
 920  vi gasteiger.cpp 
 921  git diff gasteiger.cpp 
 922  git status gasteiger.cpp 
 923  git status
 924  git diff sphere.cpp 
 925  exit
 926  home
 927  class
 928  cd
 929  ls
 930  mv class_project/ AMS_536
 931  ls
 932  cd AMS_536/
 933  ls
 934  mkdir class_work
 935  mkdir class_project
 936  cd ..
 937  cd AMS_536/
 938  pwd
 939  vi ~/.bashrc
 940  source ~/.bashrc
 941  home
 942  class
 943  ls
 944  pwd
 945  cd ..
 946  cd projects/
 947  ls
 948  cd AMS536
 949  cd zzz.programs
 950  ls
 951  cd dock6.12_ams536/
 952  ls
 953  cd bin/
 954  ls
 955  cd 
 956  man date
 957  ls
 958  cd ..
 959  cd projects/AMS536/
 960  ls
 961  cd 2025/
 962  ls
 963  cd rotations/
 964  ls
 965  cd ..
 966  ls
 967  cd 2025/
 968  ls
 969  cd additional_files/
 970  ls
 971  cd ..
 972  ls
 973  cd ..
 974  ls
 975  vi junk.txt 
 976  ls
 977  cd 2025
 978  ls
 979  cd
 980  cd ../../
 981  sinfo
 982  alias
 983  class
 984  ls
 985  cd class_work/
 986  ls
 987  touch Notes.txt
 988  vi Notes.txt 
 989  class
 990  cd ..
 991  class
 992  ls
 993  cd class_work/
 994  ls
 995  vi Notes.txt 
 996  which dock6
 997  vi Notes.txt 
 998  vi ~/.bashrc
 999  exit
1000  home
1001  module list
1002  module load git
1003  git diff
1004  git status
1005  git branch
1006  ls
1007  module list
1008  history

(base) [ehspector@login1 espector]$ git branch fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). (base) [ehspector@login1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login1 espector]$ cd builds/alpha_branch/ (base) [ehspector@login1 alpha_branch]$ git branch

alpha_branch

 master

(base) [ehspector@login1 alpha_branch]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout modified: src/dock/dock.cpp modified: src/dock/filter.cpp modified: src/dock/filter.h modified: src/dock/orient.cpp modified: src/dock/sphere.cpp modified: src/rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 alpha_branch]$ cd src/dock (base) [ehspector@login1 dock]$ ;s -bash: syntax error near unexpected token `;' (base) [ehspector@login1 dock]$ ls amber_typer.cpp filter.o mem_info.h score_internal.cpp amber_typer.h fingerprint.cpp mem_info.o score_internal.h amber_typer.o fingerprint.h nab score_internal.o base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp base_grid.h fraggraph.cpp nab.h score_multigrid.h base_grid.o fraggraph.h orient.cpp score_multigrid.o base_mpi.cpp fraggraph.o orient.h score.o base_mpi.h fragment.cpp orient.o score_ph4.cpp base_mpi.o fragment.h rddrive.cpp score_ph4.h base_score.cpp fragment.o rddrive.h score_ph4.o base_score.h gasteiger.cpp rddrive.o score_sasa.cpp base_score.o gasteiger.h rdtyper.cpp score_sasa.h conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp conf_gen_ag.o grid.h README score_solvent.h conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o conf_gen_cg.h gzstream sasa.h score_volume.cpp conf_gen_cg.o hungarian.cpp sasa.o score_volume.h conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h conf_gen_ga.cpp library_file.h score.cpp sphere.o conf_gen_ga.h library_file.o score_descriptor.cpp tnt conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl conf_gen_hdb.o lol score_footprint.h trace.o defreal.h Makefile score_footprint.o utils.cpp dock.cpp master_conf.cpp score_gist.cpp utils.h dockmol.cpp master_conf.h score_gist.h utils.o dockmol.h master_conf.o score_gist.o version.h dockmol.o master_score.cpp score.h xlogp.cpp dock.o master_score.h score_hbond.cpp xlogp.h filter.cpp master_score.o score_hbond.h filter.h mem_info.cpp score_hbond.o (base) [ehspector@login1 dock]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: ../../install/test/minimization/minimize7.dockout modified: dock.cpp modified: filter.cpp modified: filter.h modified: orient.cpp modified: sphere.cpp modified: ../rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

lol ../rdkit/boost/ ../rdkit/boost_1_71_0.tar.gz ../rdkit/boost_1_71_0/ ../rdkit/eigen-3.3.9.tar.gz ../rdkit/eigen-3.3.9/ ../rdkit/rdkit-Release_2019_09_1.tar.gz ../rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 dock]$ git diff dock.cpp diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp index 81925eac..e447b601 100644 --- a/src/dock/dock.cpp +++ b/src/dock/dock.cpp @@ -820,7 +820,7 @@ main(int argc, char **argv)

        if (c_filter.use_database_filter)
        {
            //calculate RDKIT-related descriptors for the ligand

- c_filter.calc_descriptors(mol); + c_filter.calc_descriptors(mol, c_typer);

            //other descriptors are now computed & printed in amber_typer.cpp
            //print out the descriptors
            //cout << c_filter.get_descriptors(mol);

(base) [ehspector@login1 dock]$ git diff orient.cpp diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp index 92d58f71..2d63fece 100644 --- a/src/dock/orient.cpp +++ b/src/dock/orient.cpp @@ -461,8 +461,7 @@ Orient::get_spheres()

    spheres = Active_Site_Spheres :: get_instance();
    num_spheres = spheres.size();

- if (verbose) cout << "Read in " << num_spheres - << " spheres for orienting." << endl; + cout << "Read in " << num_spheres << " spheres for orienting." << endl;

    // process critical points
    if (critical_points) {

(base) [ehspector@login1 dock]$ vi orient.cpp (base) [ehspector@login1 dock]$ vi orient.cpp (base) [ehspector@login1 dock]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: ../../install/test/minimization/minimize7.dockout modified: dock.cpp modified: filter.cpp modified: filter.h modified: orient.cpp modified: sphere.cpp modified: ../rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

lol ../rdkit/boost/ ../rdkit/boost_1_71_0.tar.gz ../rdkit/boost_1_71_0/ ../rdkit/eigen-3.3.9.tar.gz ../rdkit/eigen-3.3.9/ ../rdkit/rdkit-Release_2019_09_1.tar.gz ../rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 dock]$ cd .. (base) [ehspector@login1 src]$ cd rdkit (base) [ehspector@login1 rdkit]$ vi Makefile (base) [ehspector@login1 rdkit]$ cd .. (base) [ehspector@login1 src]$ cd dock (base) [ehspector@login1 dock]$ git diff orient.cpp diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp index 92d58f71..ff8d8a36 100644 --- a/src/dock/orient.cpp +++ b/src/dock/orient.cpp @@ -460,9 +460,9 @@ Orient::get_spheres()

    spheres = Active_Site_Spheres :: get_instance();
    num_spheres = spheres.size();

- - if (verbose) cout << "Read in " << num_spheres - << " spheres for orienting." << endl; + + // prints the number of spheres that are generated EHS 9/18/23 + cout << "Read in " << num_spheres << " spheres for orienting." << endl;

    // process critical points
    if (critical_points) {

(base) [ehspector@login1 dock]$ git diff sphere.cpp diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp index 27641d83..5739a67c 100644 --- a/src/dock/sphere.cpp +++ b/src/dock/sphere.cpp @@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )

    fclose(sphere_file);

    return num_spheres;

+

(base) [ehspector@login1 dock]$ vi sphere.cpp (base) [ehspector@login1 dock]$ ls amber_typer.cpp filter.o mem_info.h score_internal.cpp amber_typer.h fingerprint.cpp mem_info.o score_internal.h amber_typer.o fingerprint.h nab score_internal.o base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp base_grid.h fraggraph.cpp nab.h score_multigrid.h base_grid.o fraggraph.h orient.cpp score_multigrid.o base_mpi.cpp fraggraph.o orient.h score.o base_mpi.h fragment.cpp orient.o score_ph4.cpp base_mpi.o fragment.h rddrive.cpp score_ph4.h base_score.cpp fragment.o rddrive.h score_ph4.o base_score.h gasteiger.cpp rddrive.o score_sasa.cpp base_score.o gasteiger.h rdtyper.cpp score_sasa.h conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp conf_gen_ag.o grid.h README score_solvent.h conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o conf_gen_cg.h gzstream sasa.h score_volume.cpp conf_gen_cg.o hungarian.cpp sasa.o score_volume.h conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h conf_gen_ga.cpp library_file.h score.cpp sphere.o conf_gen_ga.h library_file.o score_descriptor.cpp tnt conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl conf_gen_hdb.o lol score_footprint.h trace.o defreal.h Makefile score_footprint.o utils.cpp dock.cpp master_conf.cpp score_gist.cpp utils.h dockmol.cpp master_conf.h score_gist.h utils.o dockmol.h master_conf.o score_gist.o version.h dockmol.o master_score.cpp score.h xlogp.cpp dock.o master_score.h score_hbond.cpp xlogp.h filter.cpp master_score.o score_hbond.h filter.h mem_info.cpp score_hbond.o (base) [ehspector@login1 dock]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: ../../install/test/minimization/minimize7.dockout modified: dock.cpp modified: filter.cpp modified: filter.h modified: orient.cpp modified: ../rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

lol ../rdkit/boost/ ../rdkit/boost_1_71_0.tar.gz ../rdkit/boost_1_71_0/ ../rdkit/eigen-3.3.9.tar.gz ../rdkit/eigen-3.3.9/ ../rdkit/rdkit-Release_2019_09_1.tar.gz ../rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@login1 dock]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_500 % pip install pandas --upgrade Requirement already satisfied: pandas in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (2.0.3) Collecting pandas

 Obtaining dependency information for pandas from https://files.pythonhosted.org/packages/a8/44/d9502bf0ed197ba9bf1103c9867d5904ddcaf869e52329787fc54ed70cc8/pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata
 Downloading pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (89 kB)
    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.9/89.9 kB 1.2 MB/s eta 0:00:00

Requirement already satisfied: numpy>=1.23.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (1.26.4) Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2023.3.post1) Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2023.3) Requirement already satisfied: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0) Downloading pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl (12.6 MB)

  ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.6/12.6 MB 18.7 MB/s eta 0:00:00

Installing collected packages: pandas

 Attempting uninstall: pandas
   Found existing installation: pandas 2.0.3
   Uninstalling pandas-2.0.3:
     Successfully uninstalled pandas-2.0.3

Successfully installed pandas-2.2.3 (base) supremestudier@Evans-MBP AMS_500 % polaris login /Users/supremestudier/anaconda3/lib/python3.11/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).

 from pandas.core import (

[2025-02-02 22:02:58] INFO You are successfully logged in to the Polaris client.py:252

                              Hub.

(base) supremestudier@Evans-MBP AMS_500 % python --version Python 3.11.5 (base) supremestudier@Evans-MBP AMS_500 % pip install fsspec==2024.12.0 Collecting fsspec==2024.12.0

 Obtaining dependency information for fsspec==2024.12.0 from https://files.pythonhosted.org/packages/de/86/5486b0188d08aa643e127774a99bac51ffa6cf343e3deb0583956dca5b22/fsspec-2024.12.0-py3-none-any.whl.metadata
 Downloading fsspec-2024.12.0-py3-none-any.whl.metadata (11 kB)

Downloading fsspec-2024.12.0-py3-none-any.whl (183 kB)

  ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 183.9/183.9 kB 2.5 MB/s eta 0:00:00

Installing collected packages: fsspec

 Attempting uninstall: fsspec
   Found existing installation: fsspec 2023.4.0
   Uninstalling fsspec-2023.4.0:
     Successfully uninstalled fsspec-2023.4.0

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. s3fs 2023.4.0 requires fsspec==2023.4.0, but you have fsspec 2024.12.0 which is incompatible. Successfully installed fsspec-2024.12.0 (base) supremestudier@Evans-MBP AMS_500 % conda activate (base) supremestudier@Evans-MBP AMS_500 % ls Materials Week_2 (base) supremestudier@Evans-MBP AMS_500 % conda environment usage: conda [-h] [--no-plugins] [-V] COMMAND ... conda: error: argument COMMAND: invalid choice: 'environment' (choose from 'clean', 'compare', 'config', 'create', 'info', 'init', 'install', 'list', 'notices', 'package', 'remove', 'uninstall', 'rename', 'run', 'search', 'update', 'upgrade', 'build', 'content-trust', 'convert', 'debug', 'develop', 'doctor', 'index', 'inspect', 'metapackage', 'render', 'skeleton', 'env', 'token', 'pack', 'repo', 'server', 'verify') (base) supremestudier@Evans-MBP AMS_500 % conda install fsspec==2024.12.0 Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1 done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: done

> WARNING: A newer version of conda exists. <

 current version: 23.7.4
 latest version: 25.1.1

Please update conda by running

   $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

    conda install conda=25.1.1

Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0 WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0 WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0 done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: - failed

CondaError: KeyboardInterrupt

(base) supremestudier@Evans-MBP AMS_500 % cd .. (base) supremestudier@Evans-MBP Spring_25 % pip show fsspec Name: fsspec Version: 2024.12.0 Summary: File-system specification Home-page: Author: Author-email: License: BSD 3-Clause License

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this

 list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice,

 this list of conditions and the following disclaimer in the documentation
 and/or other materials provided with the distribution.

Neither the name of the copyright holder nor the names of its

 contributors may be used to endorse or promote products derived from
 this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Location: /Users/supremestudier/anaconda3/lib/python3.11/site-packages Requires: Required-by: dask, datamol, datasets, huggingface-hub, intake, polaris-lib, s3fs (base) supremestudier@Evans-MBP Spring_25 % polaris login /Users/supremestudier/anaconda3/lib/python3.11/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).

 from pandas.core import (

[2025-02-03 15:53:30] INFO You are successfully logged in to the Polaris client.py:252

                              Hub.

(base) supremestudier@Evans-MBP Spring_25 % pip install pymol ERROR: Could not find a version that satisfies the requirement pymol (from versions: none) ERROR: No matching distribution found for pymol (base) supremestudier@Evans-MBP Spring_25 % conda activate (base) supremestudier@Evans-MBP Spring_25 % conda install -c schrodinger pymol Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1 done Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

CondaError: KeyboardInterrupt

(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Permission denied, please try again. ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@login1 ~]$ cd AMS_536/ (base) [ehspector@login1 AMS_536]$ ls class_project class_work (base) [ehspector@login1 AMS_536]$ cd class_work/ (base) [ehspector@login1 class_work]$ ls Notes.txt (base) [ehspector@login1 class_work]$ vi Notes.txt (base) [ehspector@login1 class_work]$ touch commands.txt (base) [ehspector@login1 class_work]$ vi commands.txt (base) [ehspector@login1 class_work]$ bash commands.txt (base) [ehspector@login1 class_work]$ ls 001_structure commands.txt Notes.txt (base) [ehspector@login1 class_work]$ vi commands.txt (base) [ehspector@login1 class_work]$ bash commands.txt mkdir: cannot create directory ‘001_structure’: File exists (base) [ehspector@login1 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@login1 class_work]$ exit logout (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ class (base) [ehspector@login1 AMS_536]$ ls class_project class_work (base) [ehspector@login1 AMS_536]$ cd class_work/ (base) [ehspector@login1 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@login1 class_work]$ cd 001_structure/ (base) [ehspector@login1 001_structure]$ pwd /gpfs/home/ehspector/AMS_536/class_work/001_structure (base) [ehspector@login1 001_structure]$ ^C (base) [ehspector@login1 001_structure]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ exit logout (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login1 ~]$ class (base) [ehspector@login1 AMS_536]$ cd class_work/ (base) [ehspector@login1 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@login1 class_work]$ cd 002_surface_spheres/ (base) [ehspector@login1 002_surface_spheres]$ ls 2w26_surface.dms (base) [ehspector@login1 002_surface_spheres]$ vi INSPH (base) [ehspector@login1 002_surface_spheres]$ vi INSPH (base) [ehspector@login1 002_surface_spheres]$ sphgen -i INSPH -o OUTSPH bash: sphgen: command not found... (base) [ehspector@login1 002_surface_spheres]$ which sphgen /usr/bin/which: no sphgen in (/gpfs/home/ehspector/miniconda3/bin:/gpfs/home/ehspector/miniconda3/condabin:/gpfs/software/mvapich/haswell/gcc13.2/2.3.7/bin:/gpfs/software/gcc/haswell/13.2.0/bin:/cm/shared/apps/slurm/17.11.12/sbin:/cm/shared/apps/slurm/17.11.12/bin:/cm/local/apps/environment-modules/4.0.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/4.0.0/bin:/gpfs/software/local/bin:/gpfs/projects/rizzo/espector/builds/alpha_branch/bin:/gpfs/home/ehspector/bin) (base) [ehspector@login1 002_surface_spheres]$ cd .. (base) [ehspector@login1 class_work]$ cd .. (base) [ehspector@login1 AMS_536]$ cd .. (base) [ehspector@login1 ~]$ cd .. (base) [ehspector@login1 home]$ cd .. (base) [ehspector@login1 gpfs]$ cd projects/AMS536 (base) [ehspector@login1 AMS536]$ ls 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 2020 2022 2024 get_anchors.py zzz.anchors (base) [ehspector@login1 AMS536]$ cd 2025/ (base) [ehspector@login1 2025]$ ls additional_files robbashrc_file rotations wed_humpday.txt (base) [ehspector@login1 2025]$ cd .. (base) [ehspector@login1 AMS536]$ cd zzz.programs/ (base) [ehspector@login1 zzz.programs]$ ls amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber dock6.10 dock6.12 gen-frags-12 VS_libraries dock6.10_milan dock6.12_ams536 old (base) [ehspector@login1 zzz.programs]$ cd dock6.12_ams536 (base) [ehspector@login1 dock6.12_ams536]$ ls bin developer docs install parameters README README.md src template_pipeline tutorials (base) [ehspector@login1 dock6.12_ams536]$ cd bin/ (base) [ehspector@login1 bin]$ ls am1bcc combine_torenv.py mol2bild.py parmchk showsphere amberize_complex dock6 mol2.py prepare_amber.pl solvgrid amberize_ligand dock6.mpi mopac prepare_rna_amber.pl solvmap amberize_receptor espgen mopac.sh prepgen sphere_selector antechamber grid multigrid_fp_gen.py resp sphgen atomtype grid-convert nchemgrid_GB respgen teLeap bondtype grid-convrds nchemgrid_SA sevsolv tleap chemgrid make_phimap parmcal showbox (base) [ehspector@login1 bin]$ pwd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin (base) [ehspector@login1 bin]$ class (base) [ehspector@login1 AMS_536]$ cd class_work/ (base) [ehspector@login1 class_work]$ cd 002_surface_spheres/ (base) [ehspector@login1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen) /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5) /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5) /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5) /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5) (base) [ehspector@login1 002_surface_spheres]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd class_work/ (base) [ehspector@milan1 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 2w26_surface.dms INSPH (base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH At line 328 of file sphgen.f Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:

0 0x7ffff7d59e39 in formatted_transfer_scalar_read

at ../../../libgfortran/io/transfer.c:1790

1 0x7ffff7d5b535 in formatted_transfer

at ../../../libgfortran/io/transfer.c:2491

2 0x4049e0 in ???
3 0x40516a in ???
4 0x40117c in ???
5 0x7ffff742958f in ???
6 0x7ffff742963f in ???
7 0x4011b4 in ???
8 0xffffffffffffffff in ???

(base) [ehspector@milan1 002_surface_spheres]$ ls 2w26_surface.dms INSPH OUTSPH temp1.ms temp3.atc (base) [ehspector@milan1 002_surface_spheres]$ rm 2w26_surface.dms (base) [ehspector@milan1 002_surface_spheres]$ rm temp1.ms temp3.atc (base) [ehspector@milan1 002_surface_spheres]$ ls INSPH OUTSPH (base) [ehspector@milan1 002_surface_spheres]$ rm OUTSPH (base) [ehspector@milan1 002_surface_spheres]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd class_work (base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 2w26_new_surface.dms INSPH (base) [ehspector@milan1 002_surface_spheres]$ vi INSPH (base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH (base) [ehspector@milan1 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH (base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH (base) [ehspector@milan1 002_surface_spheres]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Permission denied, please try again. ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ module load git (base) [ehspector@milan2 ~]$ home (base) [ehspector@milan2 espector]$ cd builds/ (base) [ehspector@milan2 builds]$ cd alpha_branch/ (base) [ehspector@milan2 alpha_branch]$ git branch

alpha_branch

 master

(base) [ehspector@milan2 alpha_branch]$ git pull /gpfs/software/git/2.36.2/libexec/git-core/git-remote-https: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory (base) [ehspector@milan2 alpha_branch]$ module list Currently Loaded Modulefiles:

1) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack   
2) shared                   4) mvapich2/gcc13.2/2.3.7   6) git/2.36.2

(base) [ehspector@milan2 alpha_branch]$ module unload git (base) [ehspector@milan2 alpha_branch]$ git pull Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': Updating 4be5c842..2ce698b4 error: Your local changes to the following files would be overwritten by merge: src/dock/dock.cpp src/dock/orient.cpp Please commit your changes or stash them before you merge. Aborting (base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.

 (use "git pull" to update your local branch)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout modified: src/dock/dock.cpp modified: src/dock/filter.cpp modified: src/dock/filter.h modified: src/dock/orient.cpp modified: src/rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@milan2 alpha_branch]$ git add Nothing specified, nothing added. hint: Maybe you wanted to say 'git add .'? hint: Turn this message off by running hint: "git config advice.addEmptyPathspec false" (base) [ehspector@milan2 alpha_branch]$ git add src/dock/dock.cpp src/dock/filter.cpp src/dock/filter.h (base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: ability to gasterize mols" [alpha_branch 8c38cd54] feat: ability to gasterize mols

3 files changed, 70 insertions(+), 8 deletions(-)

(base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch and 'origin/alpha_branch' have diverged, and have 1 and 267 different commits each, respectively.

 (use "git pull" if you want to integrate the remote branch with yours)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout modified: src/dock/orient.cpp modified: src/rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@milan2 alpha_branch]$ git pull Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': hint: You have divergent branches and need to specify how to reconcile them. hint: You can do so by running one of the following commands sometime before hint: your next pull: hint: hint: git config pull.rebase false # merge hint: git config pull.rebase true # rebase hint: git config pull.ff only # fast-forward only hint: hint: You can replace "git config" with "git config --global" to set a default hint: preference for all repositories. You can also pass --rebase, --no-rebase, hint: or --ff-only on the command line to override the configured default per hint: invocation. fatal: Need to specify how to reconcile divergent branches. (base) [ehspector@milan2 alpha_branch]$ git pull --rebase error: cannot pull with rebase: You have unstaged changes. error: Please commit or stash them. (base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch and 'origin/alpha_branch' have diverged, and have 1 and 267 different commits each, respectively.

 (use "git pull" if you want to integrate the remote branch with yours)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout modified: src/dock/orient.cpp modified: src/rdkit/Makefile

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@milan2 alpha_branch]$ git add src/dock/orient.cpp (base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: shows number of spheres generated" [alpha_branch 704ff10f] feat: shows number of spheres generated

1 file changed, 3 insertions(+), 3 deletions(-)

(base) [ehspector@milan2 alpha_branch]$ git add src/rdkit/Makefile (base) [ehspector@milan2 alpha_branch]$ git commit -m "fix: replaces boost url with working one " [alpha_branch 123e4913] fix: replaces boost url with working one

1 file changed, 3 insertions(+), 1 deletion(-)

(base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch and 'origin/alpha_branch' have diverged, and have 3 and 267 different commits each, respectively.

 (use "git pull" if you want to integrate the remote branch with yours)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@milan2 alpha_branch]$ git push Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': remote: Support for password authentication was removed on August 13, 2021. remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication. fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/' (base) [ehspector@milan2 alpha_branch]$ git push Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': To https://github.com/EvanS-Dock6/dock6.git

! [rejected]          alpha_branch -> alpha_branch (non-fast-forward)

error: failed to push some refs to 'https://github.com/EvanS-Dock6/dock6.git' hint: Updates were rejected because the tip of your current branch is behind hint: its remote counterpart. If you want to integrate the remote changes, hint: use 'git pull' before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. (base) [ehspector@milan2 alpha_branch]$ git pull Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': hint: You have divergent branches and need to specify how to reconcile them. hint: You can do so by running one of the following commands sometime before hint: your next pull: hint: hint: git config pull.rebase false # merge hint: git config pull.rebase true # rebase hint: git config pull.ff only # fast-forward only hint: hint: You can replace "git config" with "git config --global" to set a default hint: preference for all repositories. You can also pass --rebase, --no-rebase, hint: or --ff-only on the command line to override the configured default per hint: invocation. fatal: Need to specify how to reconcile divergent branches. (base) [ehspector@milan2 alpha_branch]$ git pull --rebase error: cannot pull with rebase: You have unstaged changes. error: Please commit or stash them. (base) [ehspector@milan2 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch and 'origin/alpha_branch' have diverged, and have 3 and 267 different commits each, respectively.

 (use "git pull" if you want to integrate the remote branch with yours)

Changes not staged for commit:

 (use "git add/rm <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

deleted: install/test/minimization/minimize7.dockout

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@milan2 alpha_branch]$ git rm install/test/minimization/minimize7.dockout rm 'install/test/minimization/minimize7.dockout' (base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch and 'origin/alpha_branch' have diverged, and have 3 and 267 different commits each, respectively.

 (use "git pull" if you want to integrate the remote branch with yours)

Changes to be committed:

 (use "git restore --staged <file>..." to unstage)

deleted: install/test/minimization/minimize7.dockout

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

(base) [ehspector@milan2 alpha_branch]$ git commit -m "build: rm minimize.docot" [alpha_branch fe018e1e] build: rm minimize.docot

1 file changed, 187 deletions(-)
delete mode 100644 install/test/minimization/minimize7.dockout

(base) [ehspector@milan2 alpha_branch]$ git push Username for 'https://github.com': ^C (base) [ehspector@milan2 alpha_branch]$ git pull Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': hint: You have divergent branches and need to specify how to reconcile them. hint: You can do so by running one of the following commands sometime before hint: your next pull: hint: hint: git config pull.rebase false # merge hint: git config pull.rebase true # rebase hint: git config pull.ff only # fast-forward only hint: hint: You can replace "git config" with "git config --global" to set a default hint: preference for all repositories. You can also pass --rebase, --no-rebase, hint: or --ff-only on the command line to override the configured default per hint: invocation. fatal: Need to specify how to reconcile divergent branches. (base) [ehspector@milan2 alpha_branch]$ git pull --rebase Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': Successfully rebased and updated refs/heads/alpha_branch. (base) [ehspector@milan2 alpha_branch]$ git status On branch alpha_branch Your branch is ahead of 'origin/alpha_branch' by 4 commits.

 (use "git push" to publish your local commits)

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

nothing added to commit but untracked files present (use "git add" to track) (base) [ehspector@milan2 alpha_branch]$ git push Username for 'https://github.com': EvanS-Dock6 Password for 'https://EvanS-Dock6@github.com': Enumerating objects: 34, done. Counting objects: 100% (34/34), done. Delta compression using up to 128 threads Compressing objects: 100% (21/21), done. Writing objects: 100% (22/22), 2.96 KiB | 2.96 MiB/s, done. Total 22 (delta 17), reused 0 (delta 0), pack-reused 0 remote: Resolving deltas: 100% (17/17), completed with 11 local objects. To https://github.com/EvanS-Dock6/dock6.git

  2ce698b4..5f99310b  alpha_branch -> alpha_branch

(base) [ehspector@milan2 alpha_branch]$ docs -bash: docs: command not found (base) [ehspector@milan2 alpha_branch]$ cd docs (base) [ehspector@milan2 docs]$ ls bugfixes610 bugfixes65 dock6_manual.html new_in_6.11.txt new_in_6.4.txt README bugfixes611 bugfixes66 faq new_in_6.12.txt new_in_6.5.txt tutorials bugfixes612 bugfixes67 faq.htm new_in_6.13.txt new_in_6.6.txt bugfixes62 bugfixes68 images new_in_6.1.txt new_in_6.7.txt bugfixes63 bugfixes69 index.htm new_in_6.2.txt new_in_6.8.txt bugfixes64 bugfixes.htm new_in_6.10.txt new_in_6.3.txt new_in_6.9.txt (base) [ehspector@milan2 docs]$ vi new_in_6.13.txt (base) [ehspector@milan2 docs]$ home (base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@milan2 gas_teiger]$ vi gas.in (base) [ehspector@milan2 gas_teiger]$ home (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs (base) [ehspector@milan2 docs]$ vi new_in_6.13.txt (base) [ehspector@milan2 docs]$ vi dock6_manual.html (base) [ehspector@milan2 docs]$ pwd /gpfs/projects/rizzo/espector/builds/alpha_branch/docs (base) [ehspector@milan2 docs]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ home (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ cd .. (base) [ehspector@milan2 rizzo]$ class (base) [ehspector@milan2 AMS_536]$ ls class_project class_work (base) [ehspector@milan2 AMS_536]$ cd class_work/ (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2 (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ vi 2w26.sph (base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphere_selector 2w26.sph ../001_structure/2w26_ligand_hydrogens_charges.mol2 10.0 (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 class_work]$ cd 003 -bash: cd: 003: No such file or directory (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ cd 002 -bash: cd: 002: No such file or directory (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ ls 01showbox.sh showbox.in (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh

automatically construct box to enclose spheres [Y/N]?
extra margin to also be enclosed (angstroms)?
  (this will be added in all 6 directions)
sphere file-
cluster number-

At line 61 of file showbox.f (unit = 1) Fortran runtime error: Cannot open file '../002_spheres/selected_spheres.sph': No such file or directory

Error termination. Backtrace:

0 0x7ffff7d54ca5 in already_open

at ../../../libgfortran/io/open.c:742

1 0x4015d9 in ???
2 0x40115c in ???
3 0x7ffff742958f in ???
4 0x7ffff742963f in ???
5 0x401194 in ???
6 0xffffffffffffffff in ???

(base) [ehspector@milan2 003_gridbox]$ ls 01showbox.sh showbox.in (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 class_work]$ cd 003 -bash: cd: 003: No such file or directory (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls 01showbox.sh showbox.in (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh 01showbox.sh: line 3: syntax error near unexpected token `&' 01showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < &showbox.in&' (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh 01showbox.sh: line 3: syntax error near unexpected token `&' 01showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < showbox.in > &showbox.log&' (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi '&showbox.log&' (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi 2w26.box.pdb (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ cd .. (base) [ehspector@milan2 AMS_536]$ tar -cvf 2w26 tar: Cowardly refusing to create an empty archive Try 'tar --help' or 'tar --usage' for more information. (base) [ehspector@milan2 AMS_536]$ ls class_project class_work (base) [ehspector@milan2 AMS_536]$ cd class_ -bash: cd: class_: No such file or directory (base) [ehspector@milan2 AMS_536]$ cd class_work/ (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2 (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi grid. (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ bash grid.sh (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi grid.out (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ bash grid.sh (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi grid.out (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2 (base) [ehspector@milan2 001_structure]$ vi 2w26_protein_with_charges.mol2 (base) [ehspector@milan2 001_structure]$ pwd /gpfs/home/ehspector/AMS_536/class_work/001_structure (base) [ehspector@milan2 001_structure]$ homw -bash: homw: command not found (base) [ehspector@milan2 001_structure]$ home (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ cd gas_test/ (base) [ehspector@milan2 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@milan2 gas_test]$ cd .. (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ cd gas_test/ (base) [ehspector@milan2 gas_test]$ vi test.in (base) [ehspector@milan2 gas_test]$ vi test_2.in (base) [ehspector@milan2 gas_test]$ cd gas_f_test/ (base) [ehspector@milan2 gas_f_test]$ ls diff.out gas_0.out_scored.mol2 gas_1.out gas_50.in gas_50.out_scored.mol2 gas_0.out gas_1.in gas_1.out_scored.mol2 gas_50.out (base) [ehspector@milan2 gas_f_test]$ vi gas_1.in (base) [ehspector@milan2 gas_f_test]$ cd .. (base) [ehspector@milan2 gas_test]$ cd .. (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ cd gas_test/ (base) [ehspector@milan2 gas_test]$ ls 4s0v_GA.in 4s0v_GA_output.restart0028.mol2 4s0v_GA.out 4s0v_GA_output.restart0029.mol2 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm 4s0v_GA_output.restart0022.mol2 charge_data 4s0v_GA_output.restart0023.mol2 gas_f_test 4s0v_GA_output.restart0024.mol2 gas_RD_Test 4s0v_GA_output.restart0025.mol2 GA.txt 4s0v_GA_output.restart0026.mol2 test_2.in 4s0v_GA_output.restart0027.mol2 test.in (base) [ehspector@milan2 gas_test]$ cd gas_f_test/ (base) [ehspector@milan2 gas_f_test]$ ls diff.out gas_0.out_scored.mol2 gas_1.out gas_50.in gas_50.out_scored.mol2 gas_0.out gas_1.in gas_1.out_scored.mol2 gas_50.out (base) [ehspector@milan2 gas_f_test]$ cp gas_1.in gas_2.in (base) [ehspector@milan2 gas_f_test]$ vi gas_2.in (base) [ehspector@milan2 gas_f_test]$ vi gas_2.in (base) [ehspector@milan2 gas_f_test]$ dock6 -i gas_2.in -o gas_2.out ^C (base) [ehspector@milan2 gas_f_test]$ ls diff.out gas_1.in gas_2.in gas_50.out gas_0.out gas_1.out gas_2.out gas_50.out_scored.mol2 gas_0.out_scored.mol2 gas_1.out_scored.mol2 gas_50.in gas.out_scored.mol2 (base) [ehspector@milan2 gas_f_test]$ vi gas_2.out (base) [ehspector@milan2 gas_f_test]$ home (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs/ (base) [ehspector@milan2 docs]$ ls bugfixes610 bugfixes65 dock6_manual.html new_in_6.11.txt new_in_6.4.txt README bugfixes611 bugfixes66 faq new_in_6.12.txt new_in_6.5.txt tutorials bugfixes612 bugfixes67 faq.htm new_in_6.13.txt new_in_6.6.txt bugfixes62 bugfixes68 images new_in_6.1.txt new_in_6.7.txt bugfixes63 bugfixes69 index.htm new_in_6.2.txt new_in_6.8.txt bugfixes64 bugfixes.htm new_in_6.10.txt new_in_6.3.txt new_in_6.9.txt (base) [ehspector@milan2 docs]$ vi new_in_6.13.txt (base) [ehspector@milan2 docs]$ class (base) [ehspector@milan2 AMS_536]$ mkdir 1086 5EEN (base) [ehspector@milan2 AMS_536]$ ls 1086 5EEN class_project class_work (base) [ehspector@milan2 AMS_536]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Spring_25 % cd AMS_536/Tutorial (base) supremestudier@Evans-MBP Tutorial % ls 2w26.box.pdb 2w26.pdb 2w26.pdb1.gz 2w26.sph 2w26_charges.pdb 2w26_ligand.pdb 2w26_ligand_hydrogens_charges.mol2 2w26_ligand_hydrogens_charges.pdb 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_new_surface.dms 2w26_protein_no_hydrogens_no_charges.mol2 2w26_protein_only.pdb 2w26_protein_with_charges.mol2 2w26_surface.dms selected_spheres.sph (base) supremestudier@Evans-MBP Tutorial % vi 2w26.pdb (base) supremestudier@Evans-MBP Tutorial % ls 2w26.box.pdb 2w26.pdb 2w26.pdb1.gz 2w26.sph 2w26_charges.pdb 2w26_ligand.pdb 2w26_ligand_hydrogens_charges.mol2 2w26_ligand_hydrogens_charges.pdb 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_new_surface.dms 2w26_protein_no_hydrogens_no_charges.mol2 2w26_protein_only.pdb 2w26_protein_with_charges.mol2 2w26_surface.dms selected_spheres.sph (base) supremestudier@Evans-MBP Tutorial % mdkir 2w26 zsh: command not found: mdkir (base) supremestudier@Evans-MBP Tutorial % mkdir 2w26 (base) supremestudier@Evans-MBP Tutorial % ls 2w26 2w26.box.pdb 2w26.pdb 2w26.pdb1.gz 2w26.sph 2w26_charges.pdb 2w26_ligand.pdb 2w26_ligand_hydrogens_charges.mol2 2w26_ligand_hydrogens_charges.pdb 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_new_surface.dms 2w26_protein_no_hydrogens_no_charges.mol2 2w26_protein_only.pdb 2w26_protein_with_charges.mol2 2w26_surface.dms selected_spheres.sph (base) supremestudier@Evans-MBP Tutorial % cd .. (base) supremestudier@Evans-MBP AMS_536 % cd .. (base) supremestudier@Evans-MBP Spring_25 % cd AMS_548 (base) supremestudier@Evans-MBP AMS_548 % ls Polaris.ipynb ligand_poses_reference_structures.zip ligand_poses_reference_structures (base) supremestudier@Evans-MBP AMS_548 % pwd /Users/supremestudier/Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_548 (base) supremestudier@Evans-MBP AMS_548 % pip install pymol ERROR: Could not find a version that satisfies the requirement pymol (from versions: none) ERROR: No matching distribution found for pymol (base) supremestudier@Evans-MBP AMS_548 % which python /Users/supremestudier/anaconda3/bin/python (base) supremestudier@Evans-MBP AMS_548 % tar -jxf pymol-X_XX-bin-linux-x86-glibc23.tar.bz2 tar: Error opening archive: Failed to open 'pymol-X_XX-bin-linux-x86-glibc23.tar.bz2' (base) supremestudier@Evans-MBP AMS_548 % conda install -c conda-forge -c schrodinger pymol-bundle Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1 done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. Collecting package metadata (repodata.json): / WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0 WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0 WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0 done Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

CondaError: KeyboardInterrupt

(base) supremestudier@Evans-MBP AMS_548 % (base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U Collecting boltz

 Obtaining dependency information for boltz from https://files.pythonhosted.org/packages/22/b3/6bbc7aaea024d3dc13abc8e94ee32df74dd63bfc016e0f87abd20d0dcbbd/boltz-0.4.1-py3-none-any.whl.metadata
 Downloading boltz-0.4.1-py3-none-any.whl.metadata (4.8 kB)

Collecting torch>=2.2 (from boltz)

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Downloading lightning_utilities-0.12.0-py3-none-any.whl (28 kB) Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)

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Downloading smmap-5.0.2-py3-none-any.whl (24 kB) Building wheels for collected packages: fairscale, modelcif, antlr4-python3-runtime, ihm

 Building wheel for fairscale (pyproject.toml) ... done
 Created wheel for fairscale: filename=fairscale-0.4.13-py3-none-any.whl size=332156 sha256=3ede1c2291f5f6b09d62a36695c4c9250859b36c640d9fcd0e2ddf99fb7a7ce3
 Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/95/ef/96/5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273
 Building wheel for modelcif (setup.py) ... done
 Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41187 sha256=ffeb8ba2c058dca784bb74a9e91f3210826944eeaece3de4c80c69a9f5659770
 Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/d2/3a/8c/e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df
 Building wheel for antlr4-python3-runtime (setup.py) ... done
 Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144554 sha256=5a4205dda4ab01f28989906b79caaca2658ccbd40e312bfcea5dd139ba8f310e
 Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/1a/97/32/461f837398029ad76911109f07047fde1d7b661a147c7c56d1
 Building wheel for ihm (setup.py) ... done
 Created wheel for ihm: filename=ihm-1.8-cp311-cp311-macosx_10_9_x86_64.whl size=194880 sha256=4937e5d722d0d8f12b399d018666e98e070d6821743b4275bb68fed2605a2a06
 Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/04/b2/4d/f14324777ef987a2137e6bd184eab20679aeadf9d3ad67d198

Successfully built fairscale modelcif antlr4-python3-runtime ihm Installing collected packages: dm-tree, antlr4-python3-runtime, urllib3, smmap, setproctitle, pyyaml, numpy, mashumaro, lightning-utilities, ihm, frozendict, einops, docker-pycreds, click, types-requests, torch, sentry-sdk, scipy, requests, omegaconf, modelcif, gitdb, einx, biopython, torchmetrics, hydra-core, gitpython, fairscale, wandb, pytorch-lightning, boltz

 Attempting uninstall: urllib3
   Found existing installation: urllib3 1.26.16
   Uninstalling urllib3-1.26.16:
     Successfully uninstalled urllib3-1.26.16
 Attempting uninstall: pyyaml
   Found existing installation: PyYAML 6.0
   Uninstalling PyYAML-6.0:
     Successfully uninstalled PyYAML-6.0
 Attempting uninstall: numpy
   Found existing installation: numpy 1.26.4
   Uninstalling numpy-1.26.4:
     Successfully uninstalled numpy-1.26.4
 Attempting uninstall: click
   Found existing installation: click 8.0.4
   Uninstalling click-8.0.4:
     Successfully uninstalled click-8.0.4
 Attempting uninstall: scipy
   Found existing installation: scipy 1.15.1
   Uninstalling scipy-1.15.1:
     Successfully uninstalled scipy-1.15.1
 Attempting uninstall: requests
   Found existing installation: requests 2.31.0
   Uninstalling requests-2.31.0:
     Successfully uninstalled requests-2.31.0

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. tables 3.8.0 requires blosc2~=2.0.0, which is not installed. tables 3.8.0 requires cython>=0.29.21, which is not installed. conda-repo-cli 1.0.75 requires requests_mock, which is not installed. spyder 5.4.3 requires pyqt5<5.16, which is not installed. spyder 5.4.3 requires pyqtwebengine<5.16, which is not installed. gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed. conda-repo-cli 1.0.75 requires clyent==1.2.1, but you have clyent 1.2.2 which is incompatible. conda-repo-cli 1.0.75 requires PyYAML==6.0.1, but you have pyyaml 6.0.2 which is incompatible. conda-repo-cli 1.0.75 requires requests==2.31.0, but you have requests 2.32.3 which is incompatible. numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.3 which is incompatible. python-lsp-black 1.2.1 requires black>=22.3.0, but you have black 0.0 which is incompatible. anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible. aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible. Successfully installed antlr4-python3-runtime-4.9.3 biopython-1.84 boltz-0.4.1 click-8.1.7 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 ihm-1.8 lightning-utilities-0.12.0 mashumaro-3.14 modelcif-1.2 numpy-1.26.3 omegaconf-2.3.0 pytorch-lightning-2.4.0 pyyaml-6.0.2 requests-2.32.3 scipy-1.13.1 sentry-sdk-2.20.0 setproctitle-1.3.4 smmap-5.0.2 torch-2.2.2 torchmetrics-1.6.1 types-requests-2.32.0.20241016 urllib3-2.3.0 wandb-0.18.7 (base) supremestudier@Evans-MBP AMS_548 % pip install --upgrade pip

Requirement already satisfied: pip in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (23.2.1) Collecting pip

 Obtaining dependency information for pip from https://files.pythonhosted.org/packages/85/8a/1ddf40be20103bcc605db840e9ade09c8e8c9f920a03e9cfe88eae97a058/pip-25.0-py3-none-any.whl.metadata
 Downloading pip-25.0-py3-none-any.whl.metadata (3.7 kB)

Downloading pip-25.0-py3-none-any.whl (1.8 MB)

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Installing collected packages: pip

 Attempting uninstall: pip
   Found existing installation: pip 23.2.1
   Uninstalling pip-23.2.1:
     Successfully uninstalled pip-23.2.1

Successfully installed pip-25.0 (base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U Requirement already satisfied: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1) Requirement already satisfied: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2) Requirement already satisfied: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3) Requirement already satisfied: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2) Requirement already satisfied: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0) Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4) Requirement already satisfied: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8) Requirement already satisfied: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3) Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3) Requirement already satisfied: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016) Requirement already satisfied: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0) Requirement already satisfied: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0) Requirement already satisfied: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13) Requirement already satisfied: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14) Requirement already satisfied: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2) Requirement already satisfied: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7) Requirement already satisfied: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7) Requirement already satisfied: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2) Requirement already satisfied: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84) Requirement already satisfied: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1) Requirement already satisfied: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (1.11.1) Requirement already satisfied: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6) Requirement already satisfied: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0) Requirement already satisfied: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3) Requirement already satisfied: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1) Requirement already satisfied: typing-extensions>=4.1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from mashumaro==3.14->boltz) (4.12.2) Requirement already satisfied: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8) Requirement already satisfied: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0) Requirement already satisfied: fsspec>=2022.5.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (2024.12.0) Requirement already satisfied: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1) Requirement already satisfied: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0) Requirement already satisfied: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4) Requirement already satisfied: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4) Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0) Requirement already satisfied: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2) Requirement already satisfied: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0) Requirement already satisfied: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44) Requirement already satisfied: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0) Requirement already satisfied: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5) Requirement already satisfied: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0) Requirement already satisfied: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0) Requirement already satisfied: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4) Requirement already satisfied: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0) Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1) Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3) Requirement already satisfied: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0) Requirement already satisfied: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0) Requirement already satisfied: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1) Requirement already satisfied: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2) Requirement already satisfied: six>=1.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz) (1.16.0) Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (3.8.5) Requirement already satisfied: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12) Requirement already satisfied: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3) Requirement already satisfied: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1) Requirement already satisfied: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->einx==0.3.0->boltz) (1.3.0) Requirement already satisfied: attrs>=17.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (22.1.0) Requirement already satisfied: multidict<7.0,>=4.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (6.0.2) Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (4.0.2) Requirement already satisfied: yarl<2.0,>=1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.8.1) Requirement already satisfied: frozenlist>=1.1.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.3.3) Requirement already satisfied: aiosignal>=1.1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.2.0) Requirement already satisfied: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2) (base) supremestudier@Evans-MBP AMS_548 % pip check tables 3.8.0 requires blosc2, which is not installed. tables 3.8.0 requires cython, which is not installed. conda-repo-cli 1.0.75 requires requests-mock, which is not installed. spyder 5.4.3 requires pyqt5, which is not installed. spyder 5.4.3 requires pyqtwebengine, which is not installed. gensim 4.3.0 requires fuzzytm, which is not installed. conda-repo-cli 1.0.75 has requirement clyent==1.2.1, but you have clyent 1.2.2. conda-repo-cli 1.0.75 has requirement PyYAML==6.0.1, but you have pyyaml 6.0.2. conda-repo-cli 1.0.75 has requirement requests==2.31.0, but you have requests 2.32.3. numba 0.57.0 has requirement numpy<1.25,>=1.21, but you have numpy 1.26.3. python-lsp-black 1.2.1 has requirement black>=22.3.0, but you have black 0.0. anaconda-cloud-auth 0.1.3 has requirement pydantic<2.0, but you have pydantic 2.10.6. s3fs 2023.4.0 has requirement fsspec==2023.4.0, but you have fsspec 2024.12.0. aiobotocore 2.5.0 has requirement botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99. conda-verify 3.4.2 is not supported on this platform (base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U --use-deprecated=legacy-resolver Requirement already up-to-date: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1) Requirement already satisfied, skipping upgrade: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2) Requirement already satisfied, skipping upgrade: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3) Requirement already satisfied, skipping upgrade: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2) Requirement already satisfied, skipping upgrade: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0) Requirement already satisfied, skipping upgrade: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4) Requirement already satisfied, skipping upgrade: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8) Requirement already satisfied, skipping upgrade: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3) Requirement already satisfied, skipping upgrade: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3) Requirement already satisfied, skipping upgrade: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016) Requirement already satisfied, skipping upgrade: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0) Requirement already satisfied, skipping upgrade: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0) Requirement already satisfied, skipping upgrade: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13) Requirement already satisfied, skipping upgrade: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14) Requirement already satisfied, skipping upgrade: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2) Requirement already satisfied, skipping upgrade: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7) Requirement already satisfied, skipping upgrade: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7) Requirement already satisfied, skipping upgrade: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2) Requirement already satisfied, skipping upgrade: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84) Requirement already satisfied, skipping upgrade: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1) Requirement already satisfied, skipping upgrade: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0) Requirement already satisfied, skipping upgrade: typing-extensions>=4.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (4.12.2) Requirement already satisfied, skipping upgrade: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (1.11.1) Requirement already satisfied, skipping upgrade: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1) Requirement already satisfied, skipping upgrade: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2) Requirement already satisfied, skipping upgrade: fsspec in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (2024.12.0) Requirement already satisfied, skipping upgrade: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0) Requirement already satisfied, skipping upgrade: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3) Requirement already satisfied, skipping upgrade: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1) Requirement already satisfied, skipping upgrade: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0) Requirement already satisfied, skipping upgrade: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1) Requirement already satisfied, skipping upgrade: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0) Requirement already satisfied, skipping upgrade: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0) Requirement already satisfied, skipping upgrade: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4) Requirement already satisfied, skipping upgrade: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4) Requirement already satisfied, skipping upgrade: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2) Requirement already satisfied, skipping upgrade: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2) Requirement already satisfied, skipping upgrade: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1) Requirement already satisfied, skipping upgrade: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3) Requirement already satisfied, skipping upgrade: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6) Requirement already satisfied, skipping upgrade: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8) Requirement already satisfied, skipping upgrade: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0) Requirement already satisfied, skipping upgrade: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44) Requirement already satisfied, skipping upgrade: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0) Requirement already satisfied, skipping upgrade: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0; sys_platform != "linux" in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5) Requirement already satisfied, skipping upgrade: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0) Requirement already satisfied, skipping upgrade: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0) Requirement already satisfied, skipping upgrade: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4) Requirement already satisfied, skipping upgrade: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0) Requirement already satisfied, skipping upgrade: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->torch>=2.2->boltz) (1.3.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1) Requirement already satisfied, skipping upgrade: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas>=2.2.2->boltz) (1.16.0) Requirement already satisfied, skipping upgrade: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3) Requirement already satisfied, skipping upgrade: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12) Requirement already satisfied, skipping upgrade: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2) (base) supremestudier@Evans-MBP AMS_548 % conda activate (base) supremestudier@Evans-MBP AMS_548 % conda env list

conda environments:

base * /Users/supremestudier/anaconda3 sage-dev /Users/supremestudier/anaconda3/envs/sage-dev

                        /Users/supremestudier/opt/anaconda3

(base) supremestudier@Evans-MBP AMS_548 % which boltz /Users/supremestudier/anaconda3/bin/boltz (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ home (base) [ehspector@milan1 espector]$ cd 4s0v/ (base) [ehspector@milan1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@milan1 4s0v]$ cd gas_teiger/ (base) [ehspector@milan1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@milan1 gas_teiger]$ cd no_charge/ (base) [ehspector@milan1 no_charge]$ ls 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in 4s0v.lig_no_charge.min_scored.mol2 gas_2.out 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2 (base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2 (base) [ehspector@milan1 no_charge]$ ls 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in 4s0v.lig_no_charge.min_scored.mol2 gas_2.out 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2 (base) [ehspector@milan1 no_charge]$ cd .. (base) [ehspector@milan1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@milan1 gas_teiger]$ vi gas.in (base) [ehspector@milan1 gas_teiger]$ cd .. (base) [ehspector@milan1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@milan1 4s0v]$ cd energy_min/ (base) [ehspector@milan1 energy_min]$ ls 4s0v.lig.min_scored.mol2 min.in min.out (base) [ehspector@milan1 energy_min]$ vi 4s0v.lig.min_scored.mol2 (base) [ehspector@milan1 energy_min]$ cd .. (base) [ehspector@milan1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@milan1 4s0v]$ cd gas_teiger/ (base) [ehspector@milan1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out (base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@milan1 gas_teiger]$ cd no_charge/ (base) [ehspector@milan1 no_charge]$ ls 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in 4s0v.lig_no_charge.min_scored.mol2 gas_2.out 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2 (base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2 (base) [ehspector@milan1 no_charge]$ cd .. (base) [ehspector@milan1 gas_teiger]$ cd .. (base) [ehspector@milan1 4s0v]$ vi energy_min/4s0v.lig.min_scored.mol2 (base) [ehspector@milan1 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/test.mol2 (base) [ehspector@milan1 4s0v]$ cd gas_teiger/ (base) [ehspector@milan1 gas_teiger]$ ls gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas.out no_charge no_gas.out test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi test.mol2 (base) [ehspector@milan1 gas_teiger]$ cp gas.in gas_2.in (base) [ehspector@milan1 gas_teiger]$ pwd /gpfs/projects/rizzo/espector/4s0v/gas_teiger (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in (base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@milan1 gas_teiger]$ ls gas_2.in gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2 gas_2.out gas.out no_charge no_gas.out test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas_2.out (base) [ehspector@milan1 gas_teiger]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ home (base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@milan2 gas_teiger]$ ls gas_2.in gas.out no_gas.in test.mol2 gas_2.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2 gas.in no_charge no_gas.out_scored.mol2 (base) [ehspector@milan2 gas_teiger]$ vi gas_2.in (base) [ehspector@milan2 gas_teiger]$ cp gas_2.in gas_3.in (base) [ehspector@milan2 gas_teiger]$ vi gas_3.in (base) [ehspector@milan2 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out (base) [ehspector@milan2 gas_teiger]$ ls gas_2.in gas_3.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2 gas_2.out gas.in no_charge no_gas.out_scored.mol2 gas_3.in gas.out no_gas.in test.mol2 (base) [ehspector@milan2 gas_teiger]$ vi gas_3.out (base) [ehspector@milan2 gas_teiger]$ vi gas_3.in (base) [ehspector@milan2 gas_teiger]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ ls 1086 5EEN class_project class_work (base) [ehspector@milan2 AMS_536]$ cd class_ -bash: cd: class_: No such file or directory (base) [ehspector@milan2 AMS_536]$ cd class_work/ (base) [ehspector@milan2 class_work]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 class_work]$ cd .. (base) [ehspector@milan2 AMS_536]$ mkdir Tutorials (base) [ehspector@milan2 AMS_536]$ mv class_work/ Tutorials/ (base) [ehspector@milan2 AMS_536]$ ls 1086 5EEN class_project Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls class_work (base) [ehspector@milan2 Tutorials]$ mv class_work/ 2w26 (base) [ehspector@milan2 Tutorials]$ ls 2w26 (base) [ehspector@milan2 Tutorials]$ cd .. (base) [ehspector@milan2 AMS_536]$ mv 1086/ 5EEN/ Tutorials/ (base) [ehspector@milan2 AMS_536]$ ls class_project Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1086 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 2w26]$ cd 001 -bash: cd: 001: No such file or directory (base) [ehspector@milan2 2w26]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2 (base) [ehspector@milan2 001_structure]$ rm *.mol2 (base) [ehspector@milan2 001_structure]$ ls (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ rm selected_spheres.sph (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_new_surface.dms (base) [ehspector@milan2 002_surface_spheres]$ ls INSPH OUTSPH sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ ls INSPH sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 2w26]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls

01showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ rm 2w26.box.pdb (base) [ehspector@milan2 003_gridbox]$ rm grid.out (base) [ehspector@milan2 003_gridbox]$ mv 01showbox.sh showbox.sh (base) [ehspector@milan2 003_gridbox]$ ls

grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 2w26]$ cd 004_dock/ (base) [ehspector@milan2 004_dock]$ ls (base) [ehspector@milan2 004_dock]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 5EEN/commands.txt (base) [ehspector@milan2 Tutorials]$ cd 5EEN/ (base) [ehspector@milan2 5EEN]$ ls commands.txt (base) [ehspector@milan2 5EEN]$ bash commands.txt (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 5EEN]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/001_structure/ (base) [ehspector@milan1 001_structure]$ pwd /gpfs/home/ehspector/AMS_536/Tutorials/5EEN/001_structure (base) [ehspector@milan1 001_structure]$ cd .. (base) [ehspector@milan1 5EEN]$ cd 001_structure/ (base) [ehspector@milan1 001_structure]$ ls 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd .. (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 5een_surface.dms (base) [ehspector@milan1 002_surface_spheres]$ vi INSPH (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls INSPH sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cp 2w26/002_surface_spheres/sphere.sph 5EEN/002_surface_spheres/sphere.sph (base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 5een_surface.dms INSPH sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph

Press ENTER or type command to continue (base) [ehspector@milan1 002_surface_spheres]$ bash sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ ls 5een.sph 5een_surface.dms INSPH OUTSPH sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 5een.sph 5een_surface.dms INSPH OUTSPH sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls INSPH sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 5een.sph 5een_surface.dms INSPH OUTSPH sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 5EEN]$ cd 001_structure/ (base) [ehspector@milan1 001_structure]$ ls 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd .. (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ bash selected_sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ ls 5een.sph INSPH selected_sphere.sph sphere.sph 5een_surface.dms OUTSPH selected_spheres.sph (base) [ehspector@milan1 002_surface_spheres]$ mv selected_sphere.sph select.sph (base) [ehspector@milan1 002_surface_spheres]$ vi selected_spheres.sph (base) [ehspector@milan1 002_surface_spheres]$ cd .. (base) [ehspector@milan1 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan1 5EEN]$ mv 004_dock/ 004_energymin (base) [ehspector@milan1 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan1 5EEN]$ cd 003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ vi showbox.in (base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ ls

grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/showbox.sh 5EEN/003_gridbox/showbox.sh (base) [ehspector@milan1 Tutorials]$ cd 5EEN/ (base) [ehspector@milan1 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan1 5EEN]$ cd 003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ ls showbox.in showbox.sh (base) [ehspector@milan1 003_gridbox]$ vi showbox.sh (base) [ehspector@milan1 003_gridbox]$ bash showbox.sh (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ vi grid.in (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   grid.in   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ rm grid.in (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ ls

grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ vi grid.in (base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.in 5EEN/003_gridbox/grid.in (base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.sh 5EEN/003_gridbox/grid.sh (base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 5EEN]$ cd 001_structure/ (base) [ehspector@milan1 001_structure]$ ls 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd .. (base) [ehspector@milan1 5EEN]$ cd 003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ vi grid. (base) [ehspector@milan1 003_gridbox]$ vi grid.in (base) [ehspector@milan1 003_gridbox]$ vi grid.in (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ vi grid.in (base) [ehspector@milan1 003_gridbox]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/ (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan1 003_gridbox]$ vi grid.sh (base) [ehspector@milan1 003_gridbox]$ bash grid.sh (base) [ehspector@milan1 003_gridbox]$ ls

5een.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
grid.bmp       grid.nrg   grid.sh   '&showbox.log&'

(base) [ehspector@milan1 003_gridbox]$ vi grid.out (base) [ehspector@milan1 003_gridbox]$ cd ../004_energymin/ (base) [ehspector@milan1 004_energymin]$ ls (base) [ehspector@milan1 004_energymin]$ touch min.in (base) [ehspector@milan1 004_energymin]$ ls min.in (base) [ehspector@milan1 004_energymin]$ dock6 -i min.in

DOCK v6.12

Released April 2024 Copyright UCSF

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):yes
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Molecule Library Input Parameters

                                            ligand_atom_file [database.mol2] ():../001_structure/5een_ligand_H_cH.mol2
                                           limit_max_ligands [no] (yes no):
                                               skip_molecule [no] (yes no):
                                          read_mol_solvation [no] (yes no):
                                              calculate_rmsd [no] (yes no):yes
                                      use_rmsd_reference_mol [no] (yes no):yes
                                     rmsd_reference_filename [ligand_rmsd.mol2] ():../001_structure/5een_ligand_H_cH.mol2

Database Filter Parameters

                                         use_database_filter [no] (yes no):no

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):no

Bump Filter Parameters

                                                 bump_filter [no] (yes no):no

Master Score Parameters

                                             score_molecules [yes] (yes no):yes

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):
                                    grid_score_rep_rad_scale [1] ():
                                        grid_score_vdw_scale [1] ():
                                         grid_score_es_scale [1] ():
                                         grid_lig_efficiency [no] (yes no):
                                      grid_score_grid_prefix [grid] ():../003_gridbox/grid

GIST Score Parameters

MultiGrid Score Parameters

Dock3.5 Score Parameters

Continuous Energy Score Parameters

Footprint Similarity Score Parameters

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

                                             minimize_ligand [yes] (yes no):
                                      simplex_max_iterations [1000] ():
                              simplex_tors_premin_iterations [0] ():
                                          simplex_max_cycles [1] ():
                                      simplex_score_converge [0.1] ():
                                      simplex_cycle_converge [1.0] ():
                                          simplex_trans_step [1.0] ():
                                            simplex_rot_step [0.1] ():
                                           simplex_tors_step [10.0] ():
                                           simplex_final_min [no] (yes no):
                                         simplex_random_seed [0] ():
                                       simplex_restraint_min [no] (yes no):yes
                               simplex_coefficient_restraint [10.0] ():

Atom Typing Parameters

                                                  atom_model [all] (all | united):
                                               vdw_defn_file [vdw.defn] ():defn
                                              flex_defn_file [flex.defn] ():defn
                                             flex_drive_file [flex_drive.tbl] ():defn

Molecule Library Output Parameters

                                       ligand_outfile_prefix [output] ():5een.lig.min
                                         write_mol_solvation [no] (yes no):
                                          write_orientations [no] (yes no):
                                       num_scored_conformers [1] ():
                                             score_threshold [100.0] ():
                                                rank_ligands [no] (yes no):

Could not open defn for reading. Program will terminate.

(base) [ehspector@milan1 min.in (base) [ehspector@milan1 (base) [ehspector@milan1 (base) [ehspector@milan1 (base) [ehspector@milan1 ~]$ ls AMS_536 miniconda3 (base) [ehspector@milan1 ~]$ cd (base) [ehspector@milan1 ~]$ ls AMS_536 miniconda3 (base) [ehspector@milan1 ~]$ cd .. (base) [ehspector@milan1 home]$ ls cd ..aaachase aaaggarwal dbobo aaaggarwal.26FEB2020 dcalabria aabdurrob dcazorla aabhilash dcbrown aadarsh dcharan aadubois dchien aagashe ddassanis aagishtein ddelayo aahern ddemartini aaiyer ddukes aajith deachen aakale decarlson aakiti dekblom aakkumar delam aaksenova demccabe aaliang dereliu aallin deroy aallu devlin aalpern dfarahmandpo aamahmood dfei aambrown dfucich aamgalan dgaidhani aaminev dgenet aamurthy dgersappe aanaggarwal aanagnostopo aanik dgnatenko aaprasad dgoon aarasappan dgruzdev aarefin dgursoy aarmas dgwood aarroyave dhailegeorgi aasim dhamam aaslov dhandzlik aates dhdesouza aaurora dhildreth aavadhani dhongyi aavira dhperumal aaydin dhualong aaysheth diannace ababbar disandovalch abadhe diwliu abahadori djagnarain abaidya djgold aball djlambert abardizbania djoh abbhaskar djulian abeahmad djyu abenslama dkadams abialkowska dkharzeev abjoshi dkirby abkanevsky dkozakov abogetti dkunjadiya aborad dlanger aborcatasciu dlhe aborger dlucksted aborowicz dmahalli abozin dmahzabin abphilip dmale abrady dmarkov absalem dmarr abtambe dmckinnon aburford dmirfenderes acage dmorenosanti acalder dmukherjee acali dmulbagalven acamino dnanjappa acastiblanco dnimatullo accapua dnterry acchakravart dobyrne acherath dochoi achouhan dofu acmarra dohhlee adamare dokkang adanial dongsong adanoji dongwhan adharan donshi adiloreto dotan ading doyjang admannino dozhong adpeng dpadhorny adpollack dpare adrana dparedesmeri adrflorio dparwana adrogers dpati adubey dpatil adutt dpenchoff aecuomo dpfennell aeichert dpotemkin aeltareb drendina aeweiss drhamilton afahmed dschneble afarhadzadeh dseddoh afgregory dsforza afrigo dshangase afurey dsingla agaffoor dsli agaikwad dslo agarforth dsmolarski agargueta dstepanenko agauer dstrenski aghai dswesty agilgomez dthanassi agmaharaj dtpham agnsinha dtsybychev agopalkrishn dtung agraikos duwwang agugel dvahabli agulhane dvyas ahalwah dwhitty ahc dwiczer ahmkhan dwillcox ahomayounnik dzavala ahsingh dziadlou ahurtado eadas ahxiao earavera aicheng eatkinson aidnani ebagherizade ailyu ebartlett airussell eboria ajacovelli ebreen ajalwan ebremer ajamieson ebrini ajasniew ebryski ajchan ecarcelespov ajchavez ecgross ajhong echurch ajkoller eclemmon ajlli ecline ajmasella ecoutsias ajoung ecowley ajscarlatos edeturk ajtran edma ajwelsh edowney ajyadav edzhang akalugade eeryildiz akanodia efinson akapote egebb akarkare egentles akarzai egouvis akaufman eheywood akhibovska ehspector akhosronejad ejcarey akhoukhi ejguan akingan ejli akirillov ejohnfelt akkale ekandov akonosky ekbetancourt akravchuk ekeck akrowe ekeough aktyagi ekhew akucich eklau akuduregundi ekoo akundhuru elari akverma elettieri akwakye elgchan alabella elharris alaing eli alanhuang ellai alchung elleisenberg aldong elmlowe aldraper elogeswar alehsu elslattery alem emacosta alexhernande emarants alfwu emarkowitz algrullon emarzigliano alhhuang embriggs alianwar emrlin alicwang emroberts alietzau emyhand alifeng enebet aliguori eoruro alindquist eozkirimli allekim epapadopoulo allelin erandhawa allwong eraut almabraham erbraun almishra erfan alokre erglukhov alowell ericlin1 alperezmendo erizhou alqin erkumar alsli erluo alvhsu erosenberg alynegron errjones amacinnis erschroeder amaffei erwhuang amanagarwal esahin amanpsingh esalman amanzoor esaraivanov amaresca eschiltzrous amarya eshaji amassari eshetreatkle amasuno eshih ambbrown eshuryak amccumber esicoli amcelroy esiegmann amchale esogut amcpherran esonmez amehla essingh amehmood eswong amgondal etakeuchi amibrahim etalis amigues etchan amisaha etcheung amkgupta ethresher amnoonan etmonaco amohamed etrommer amohammadrez etsang amohanty etwest amohideen etyen amoonilal evalin amrabet evaxie amramroop evergaracobo amrangwala evxie amritpsingh ewpeterson amullhaupt exiu amychen5 eylei amyla eyzhu anadelgado fabdinov analekseenko faliang anarora falmodaresit ancollins faluo andcheung fang1 andguo fanliu2 andgutierrez fannli andrchu fanwang1 andrwu faoki andylin2 faslanbeigi anearora fatrahman anegi fatsai aneiman faye anejoshi fayyang anejoshi.OLD fbasharat anemajerova fbischoff anfrenkel fcherat angderosa fcornejofern aniksingh fcoskun anisrinivasa feliang anjmoore fenzhang ankmaheshwar fewang ankrishnan feyeh anltran fgao annicoll fhchaudhry anpnguyen fiburke anpurwar fiowong ansabharwal fjalia ansgandhi fjangchup anshen fkarankumar anslade fkhondker anthochen fladeind antmunoz fluo antzhu fmaisha anurizada fmlopez anvinod fmnoor anzaman fnieto anzhu forabona anzzhou fpocaamoros aokisamen frdominguezg apaddayurush frhu apaddayurush.OLD frobayobohor apagarwal fsotiropoulo apalit fuliang apalo fwelcome apalve fzali apamfilie gacolella aperezantona gahuja apettenati gakapoor aphope gakhan apilco galing apizzulli garrchen aplu gashna apolanco gatran apopoviciu gaumoithe aporripiredd gazzhang aprabhakar gbalabhadra apradeep gbalazsi aprencis gbangera apsinghal gbermejo apytel gbhattachary araghani gbiselli arahimyar gbock arahmati gbosilca aranasinghe gbrill aravula gchurchill arbalasubram gcma arcurtis gdhama ardasgupta gdjones ardowling gduarteramos areisel geliang aresnick gfiakos arfali ggandem argiannakopo ggeorgi arglenn ggopalkrishn arhossain gguleria arjain ghe arjkrishna ghothi armishra gibrown arobert gigill arodriguezd gimbriano arojain gipark arpahlavan girizzo arpbanerjee gito arpereira gjfuentes arsaxena gjiang arskhan gjkim arumar gkementzidis aryshrivasta gkowzan asadana glarangeira asaji gmichaels asakhan gmihalache asamala gmiles asamanta gmogol asamavedam gmoutsanidis asatam gmuradas aschneble gnarh aschorer gnwood ashaalan goconrosario asharfuddin gparkar asheneman gperezgonzal asillato gprachi asingal grahme askamat grapacciuolo askong grkulkarni asmit grperlman asofianopoul gsantucci asotocambres gsbeglia asoubki gshivakumar asparikh gshu asrivastava gstokes asugumar gsuczewski aszekely gtaylor atannenbaum guayang ataouil guayu ateklu guazeng ateplukhin guffeng athatikunta gurpreetsing athennarasu guwechue athonis gvaillant atosolini gverma atpradhan gvorobyev atripoli gyoun atsegaimoore gyzhang atsenthilnat gzakharov atvarghese gzborovsky aubutt haawilliams audupashanka haenalee auhhuang hagguo avaradarajan hahkhan avisingh haichwang avonalbertin hailxu avonderlinde hakcakaya avpatil hallu avperry hamorales awalling hanhan awardah hanschoi awgriffith hanxwu awills hanzhou1 awjohnso haochuwang aydas haolin1 ayedageresud haolyu ayedlarajaia haorazhang ayendluri haotxu ayepuri haowezheng ayreddy haoyzheng aysaleem haraja ayshim harbhatt ayusrivastav harlee aziafat hasaadi azuzow hasmoon babrahall hayyan bagarcia hazhan ballam hbchao baminazad hbien bangchen hborchert bastark hchawla bavinash hchenwu bbelisle hdle bboysan hdonga bbrendan hduong bbulag hechu bchauhan heekwon bciranni henrwang bclevine hetariq bcolle hewwang bcuadrado hhyao bdanna hipham bdarapu hjlynch bdebarrosfer hjtrivedi bdelamonica hjudson bding hkaddour beckert hkamran bejean hkhazaei bennliu hkirby benyu hle bessuman hleung bewwong hmainguy bewwu hmdonaldson bezzheng hmoonam bfei hmoura bfeole hnegi bfochtman hniederhause bfogg hnnguyen bfutcher hoannguyen bglevine hogao bgoncalves hokwak bgourbal holiver bgoyal honghuang bguruvayoorm honglliu bharrell honglu bhkumar hongwchen bhowlader hongyuli bhshin honhuang bhsiao hotnguyen bighimire hppatil bihyu hqaiser binnchen hranjan binzhou hridout bishi hrmohammed bisshrestha hrrajput bji hsarkar bjkramer hschang bjlai hsekino bjlee hseyyedzadeh bjnelson hshafiq bjqi hsiachang bjugan hsingathala bkhanikaev hsirotkin bkovarovic hsnyders blanunez htalavera blukacsy huang54 bluy huaxiao bmahal huichen5 bmariano huideng bmchapman huidliu bmhenn huisong bmhyland huixu1 bmkaufman huixzhu boakley hullee bocao hungwchen bohhuang huntwale boisuh huyzhang borwang hvannieuwenh bossun hvig bowusufrimpo hvijayakumar bozhao1 hwoh bpamuk hxing bpilosov hyejichoi bquang hyemkim bquang.OLD hyeocho brampanellid hyeonkyung brbartlett hykoo brgraham hymin brlai hyochung brlgonzalez hyuchung brma hyulim brmcgovern hyunjuncho brmoses hyunsikim brpark hzhan brsantos hzohair brshao iabbasparker brwwang iakgun bryang iakim brzhou ialabed brzhu ibilkhu bsbernstein ibipul bschiller ibolger bsen ibromberg bshan icisternino bsheller ifaridi bsheridan igkane bspitzbart igrehn bsterling ihubbard bsundahl iinani btenreiro ijacob btmichalowic ijhuang buli ikao bvilla ikotler byungjkim iloop caaugustine ilopezcoto caaventura imarchitelli calyu inikiforakis camcdonough iojima caponteriver iosipitan caprea iouthwaite cargomes iparaskevako carhall ipjohnson carlliu ipunn carlopez iramakrishna carty ishin cballena isiergiej cbehan istaylor cbetz itaradachuk cblackwell itrivedi cboon iurbinahenri cbrandon ivalin cbudd ivanlin cbunner ivaratharaja ccardetti iwankavala ccarew jaapatel ccdressler jabauer ccgordon jabryan cchecastaldo jacacosta ccioffi jaccao ccolosqui jackili ccorbo jacobsmith ccpeterson jacojoseph cdehury jacparker cdehury.OLD jacsegal cdelorenzo jaejeong cdreyer jaevangelist cegarrison jaeyojung celkhoury jafinn cexu jafu ceyeung jagluzman cfeldman jaharora cflagg jahua cfnapoli jaimehta cfontanini jakaczmarzyk cforan jakhil cgarybicas jakkatz cgauthier jalbanes cgobler jalbertigles cgrieco jalzamoramar cgueli jamarini cguerraamori jamoscosonun chacho jange chahan jannguyen chalpern janswong changhpark jaschow changjli jashukla chanzhang jasjiang charwong jasolau chccai jasonwang chdang jaswsingh chen110 jathoffman chen147 jaygutierrez chen15 jazpurua chen157 jbak chen175 jbakalis chen181 jbalsamo chen182 jbarrantes chen32 jbarron chen77 jbernauer chencjiang jbeutel chenclu jbhambure chenczhu jbickel chenghli jbkelly chengklin jbohne chengpsun jbraick chenliang jbrimlow chetheringto jbrunelle cheye jbuckley chezheng jbuckley.OLD chgraham jburzachiell chguo jcano chhhogan jcaputi chichiang jcassella chienlee jcespedes chihhchang jchaillet chihu jchivu chiuyu jchlee chlow jcmichel chmorales jcodere chodgdon jcolaizzo chou jcollier chriskim jconesa christwong jdarling chtian jdcraig chuahuang jdeneau chugo jdesilva chuntchan jdovi chuzhu jdscully chuzou jdubnau chyou jdwarren chyyoon jecao chzuo jefzhong cikang jegaillard ciriccio jejchan cjbyrnes jelau cjzheng jelsoudy ckapre jemak ckarwan jemchen ckelton jenfu ckochath jepace cksullivan jerlin cleeliang jeryeung clegett jesgoldstein clfischer jeslong clongarini jessewang clsears jettran cltong jevalle cltucker jeyeung cluhmann jeyyoo clwolfe jfmoon cmack jgaige cmcarey jgajello cmcgrew jgergen cmehndiratta jglazar cmflynn jglimm cmfoley jgurevitch cmjurgensen jhajagos cmkennedy jharder cmoczygemba jheerwig cmoote jheinz cmorantesari jheraghty cmwoo jhjung cnoe jhollister cnoutsos jhpark codlam jiabwang cohwarner jiachzhu cojiang jiacxu cokeoma jiahuwang coleary jiajgao concao jiaji conliu jiakwang cpercival jialai cpethe jialin1 cpinizzotto jiamili cplizio jiamwu cprasad jianfeng cqiu jianflin cradke jianhan crcollinswor jianjliu crfernandesv jianmtan csangiovanni jiannyang csantoni jianxiozhang csasmith jiaojiang cschwaner jiapatel cshiveshwark jiasu csiebor jiatian csimmerling jiawang1 csingleton jiaweichen cstussman jiawezhu csyreilly jiaxuyu cthakur jiayeguo ctinker jiayyan ctustin jibbai cuwang jichao cvorkas jiddong cweistuch jiechen3 cwoellhof jiemchen cxi jiemzeng cyanagisawa jienzhu cyluo jieyang cyoungflesh jihlin czhen jihoopark d9wang jihuynh dabelinsky jihyepark dagolden jiikim dagrange jijin daiwang jilao dalpancakmak jiliu1 damcintyre jimlin damiruddin jimun damoses jin dandrew jinghzhou dangelidis jingwenli danieliang jingwezhang danitorresra jingwliu danizheng jinkokim dantorres jinwang2 dantyu jinwei danwei jinyhu daoconnell jinyinwang dappark jinyli darkow jinyuyang darlin jinyxu darvind jinzwang darzeng jiqian dathanasakos jiychong daultmccoy jiyim davidlin jiyjung davizhao jiyounpark davliang jiyuliu davsilverman jiyuyang dawan jjcarter dawei jjguo dawendt jjjones dawhu jjnielsen daxxie jkable dayeung jkiryluk dayyan jkodner dayyoon jkohara dbasu jkonopka (base) [ehspector@milan1 home]$ cd .. (base) [ehspector@milan1 (base) [ehspector@milan1 AMS536]$ ls 2017 2019 2021 2023 2025 2018 2020 2022 2024 (base) [ehspector@milan1 (base) [ehspector@milan1 amber16 dock6.11 de_novo_anchors dock6.11_alpha dock6.10 dock6.12 dock6.10_milan dock6.12_ams536 old (base) [ehspector@milan1 (base) [ehspector@milan1 bin docs parameters developer install README src (base) [ehspector@milan1 (base) [ehspector@milan1 1 antechamber chem.defn chemgrid chem_match.tbl leap flex.defn flex_drive_mod.tbl flex_drive.tbl flex_just_OH.defn ph4.defn flex_mod2.defn flex_mod.defn fraglib_ga_scaffold.mol2 (base) [ehspector@milan1 /gpfs/projects/AMS536/zzz.pro (base) [ehspector@milan1 (base) [ehspector@milan1 AMS_536]$ ls class_project Tutorials (base) [ehspector@milan1 (base) [ehspector@milan1 (base) [ehspector@milan1 (base) [ehspector@milan1 (base) [ehspector@milan1 bin docs parameters developer install README src (base) [ehspector@milan1 (base) [ehspector@milan1 bin]$ ls am1bcc dock6.mpi amberize_complex espgen amberize_ligand grid amberize_receptor grid-convert parmcal antechamber grid-convrds parmchk atomtype make_phimap bondtype mol2bild.py chemgrid mol2.py combine_torenv.py mopac dock6 mopac.sh (base) [ehspector@milan1 bin]$ pwd /gpfs/projects/AMS536/zzz.pro (base) [ehspector@milan1 bin]$ class (base) [ehspector@milan1 (base) [ehspector@milan1 (base) [ehspector@milan1 004_energymin]$ ls 004_energymin]$ vi min.in 004_energymin]$ cd ../../ Tutorials]$ cd ../../ Miniconda3-latest-Linux-x86_64.sh Miniconda3-latest-Linux-x86_64.sh dbluestein jkottmann msavenkov skomatireddy jksullivan msayana skoppuravuri jktsui msazonova skorada jleehand mschedel skotelnikov jlfong mschrimpf skotla jlguerra mschwaller skrichevsky jlipshultz mshaaban skristam jlomanto mshahneousba skrupp jluceno mshih sladerwager jlungu mshinder slakshminara jlutsky mshu slaverty jlweissman msilfies slthomas jmaghakian msmoawad smadishetty jmarcantonio msrao smaiti jmarciano msreeves smallipattu jmayortorres mstanacevic smamalis jmeliker msweber smartynenko jmendezmende mtalukder smascarenhas jmgentile mthu smconnors jmiao mtoledorozyc smdick jmitchell mtsonev smedved jmorkos mturk smeghdadizan jmulackal mumarani smelhiraj jmurrugarral muprit smesiha jmurzaku mvalakonda smhenry dg-mgmt1-auth-keys jmvasquez mvashishtha smiduthuri dg-mgmt2-auth-keys jnassar mvfernandezs smilakovic jnatarajan mvilensky smirghafouri jnery mwilking smirroshande jnicasio myarif smofakham jnmauro myearsley smui jnong myoungblood smukherjee joawilson mysql smvaccaro jocai mzamani snarmeen jocwilliams mzepedaaguil snigam jodey mzhang snikhil jodoh naahassan snimatullo jodweinstein nabchowdhury snizambad joeleung nabsyed snolas joeychan nacchen snyman jofranklin nacharya soba johbernard nagnihotri sochakrabort johnliu nagutierrez sohshin joifan nalewis sohtsuka jomyoung nanqwang solhapark jonamartins napopova somishra jonicholson naqiu somunoz jonsu nasweet sooapark jonyin natsai sopjang joolee nazzhou sortizbetanc joosuh nbalasubrama sosarangi joroiland nbasok sosuresh joshmathew nbayas sowu joshumartin nbodduluri sozturk jovvazquezri nbosviel spaci joying nbowers spandrekar jozhao nciotoli spang jpantano ncmeloottu spapazahario jparise ncpathak spapazis jparkinson ndcertain sparvathredd jpascal ndev spathrose jpcastillo ndheilly spilkey jperezrios ndigrandi spiret jpeshansky ndnguyen splee jpitt ndokania spochron jpmoryl ndurand spothumahant jporavanthat ndzikowski spriyadarsha jpwhite nesteves spugach jqxiao nexposescan sqavi jranjan neyang srahmani jrawski nezheng sraisinghani jrcheung nfaiza sramanarajan jrcorbett nfpugliese sramanarajan.OLD jrest nganu sramjan jrgorman nghoang sramstrom jrimel ngitman srashidian jrkamler ngluck sretineni jrleeman ngujarati srgupte jrojahn nhamdan srnalluri jrutledge nhirtle srpayne jrwei nichaturvedi srshende jsaldivar nidimeglio ssabaghian jsalley nigreen ssagynbayeva jsaltz nileong ssandal jsaputo niranmanesh ssarnot jsaxena nisankar ssarwar jscanderson nisong sseepersaud jschuchart nisoni ssemerkant jschwedes nivsingh sserbin jseeliger njschwartzap sshaharia jseol nkahmed sshapourmian jsgordon nkandru ssheikhi jsinanan nkatla sshoque jsistla nkdean sshrestha jskowalski nkeer sshrivastava jslogan nkhalsa ssivalenka jsmaers nkhandagale ssjohn jsmucker nkhatri sskiena jsteier nkinalis ssomani jsuchan nkinlock ssperrottet jtalaveragre nkyose sstoller jtekverk nleak sstoyanov jtepan nlogozzo ssundar jtevans nlrogers ssunia jtgabrielli nmahamud ssyedfahad jtjones nmaher ssyritsyn jtmessina nmanzella staralekar jtrelewicz nmarcella stawong jtrue nmathew stelehany juaalcantara nmehanna sthaker juffeng nmeister sthorgusen julima nmenasche stjjiang juliwu nmendiratta stmandell jumma nmeruva stmccabe junding nmichielsen stomar jungshwang nmitra stpak junholee nnadkarni strainer junhuzhang nnaitlho ststern junhyelee nnakka stuznik junjiang nnawal stzeng junkang nnehaindrani stzou junszhou nnghiemvu sudkhan juntyao nniemiec sukkumar junwang5 noibrahim sunarasimhas junxialiu nolconner sunarasimhas.OLD junywang novsingh sunghucho jusandoval npahlavan sunkim2 juschan npanagodawet surmy jusliu nparghi sushahid jusong npasari suwei justili npayen svadnerkar jusu npomata svaldez juychen npregosin svanderpoel juyyan nrajput svayasi juzou nramdin svee jvansnellenb nreaton swaxman jvaska nsalekfarama swchaudhury jverbaarscho nsampson swen jvishal nsehgal sweverma jvpepe nshouman swpaul jvu nsimakov sxchen jwahhab nsipperly syaddanapudi jwcross nsmehta syalla jwcusick nsoder syarma jwisdom nsokolow syatigala jwlodek nsomani syatskar jxue nstreb sydiaz jyerrick ntadler syousef jyluo ntardugno sytlee jzoodsma ntetrault tabhatia kabichandani ntippabhatla tadoyle kadeng ntripti taeklee kadiallo nvafaeinajaf taeyounkim kadill nvitek tagiles kadreher nvohra tahkhan kafarber nvsutherland tajjung kaifzheng nwein takther kaili nwweber talama kailiu2 nxlee talare kailjiang nyfletcher talin kaimxu obellinson tallison kaitong odeshpande tamislam kaixichen odiamond tanis kamhassan odickerson taryu kamrivera oeskiocak tbabu kanagarwal ohaputhanthr tbertino kanzhao ohyejin tbrackins kapatel okim tbrinckmann kaporter okoren tbrinkley kapu omcgranaghan tburfeind karamachandr omorozova tbushra kargill omoy tcanli kasong onatu tchatterton katalwar oogunfolakan tchristy katschmidt ooreilly tchugh kbaylous orambow tcotroneo kbdiaz osdeshpande tdawar kbeckerredd oshakkour tdiprima kbelfon oshetty tdviri kberard osteele tema kberghaus oyang testro kccoughlin oyasar tgavryshko kchetan padari tglotch kchitale paggarwal tgrgas kdas pahan tgrossberndt kdavidson pallen tguttula kdehmelt pamishra thamada kdemir parjain thausch kdevedzhiev parmitage thdavidson kdhar patflanagan therault kdhuri patmuller therodrigues kdyro pavkirkar thollis kebui pavnkaur thomlin keckartt pawu thren kelam payao thzhou keliao pb tianyuawang kellywang pbaliga tili kelvlin pcascantebon timji kenchin pcastillo timshi kenhu pchinthamred tinggao kennwu pdalaya tinghwu kereid pdamore tingliu2 kerwood pdevarajan tingslin kevazquez pdjuric tinliu kevcai pdonat tiwwong kevcheng pdongle tixi keviliu pdutta tiyuan kevwei pechang tjarrett kexi peihsieh tjohannessen kfatema peinwang tkarwal kfernando penzhang tknoll kflora pesun tkohlmann kfryer pferrero tkral kgarg pgaikar tkurc kgayadhankar pganapathi tla kgcassar pganesh tlata kgjonas pgodoy tloden kgoranta pgoldbart tlonsway kgulati pgoriparthi tmcgee khajny pgubbala tmia khasegawa pguo tmohandas khoh pgurung tmoriya khumphries phariprasad tmsmyth khyunjae phowlader tmuntean kihan phtnguyen tnle kim128 phyeh tnsingletary kim169 pinlee toneal kim65 pinliu toye kingle pkaelbling tpalit kipoon pkayedpour tqduong kisrani pkidambi tqle kissung pkottapalli traj kjamal pkrstic trichen kjayanettiar pkuan trli kjroberts pkwoczak trosenlicht kjtorres pliu tsclement kjun plorenagodoy tshrestha kkamate pmao tsinghal kkannapur pmarla tslewis kkasarapu pmatera tsmiley kkasavajhala pmcdowall tteng kkaushik pmdunge tthakir kkayang pmeade tthulasidas kkirane pmeda ttnnguyen kkostyszyn pmmehta ttom kkui pmscully tweinacht kkurti pmuzac tweiwei kkyeong pnalluri twymore klanzetta pnookala txiang klhudson podonnell tye kljjohnson ppolak tyeh kllivichuzca ppriyadarshi tyokoyama kmadanahitib praagarwal tzwei kmardysilofa pragupta uarora kmasarik praroy uarora.OLD kmbala pratagarwal ugarg kmchang pratkumar ukadakia kmchau priyjain umoll kmcneil prkkumar umukherjee kmfallon prmukhopadhy upoddar kmhayes prouth urasheed kmsimon prreddy urehman kmueller psahu urosani kmungsoo psamang ushafiq kmurgas psangtani ushassan kpallmann psekar usunar kpinzon pshanbhogue utegshbayar kpipitone pskota utumuluri kprose psmeyer uuckun kralbano psokol uyevarouskay kramcharan psonawane vachandramou krayfield psoundarapan vadabala krdonaldson pssingh vanlin krisharma psurana vanugu krjain psutter vassingh krkehrli ptitle vbabu krmartin ptonra vbayevskiy krokosz ptubiolo vbrill krtan puzheng vcacciola ksabo pvaishnavi vcarter ksampathkuma pvaska vchanana kscardigno pvemula vduncan kschweitzer pvespe verana kshima pximello vgoel kshou pyao vhattibettam ksirapu pzbarrett vhegde ksoumahoro qiangwang vhnguyen kspuhler qianywu vhuynh ksucich qiaocwu vicdai kswayze qicao vidong ktallman qiding viguo kthilanka qihlin vikamat ktsteven qinie villi ktuzinowski qinjiang vima kuagarwal qinren vincewu kuchan qinzhao vinmirandabr kumar1 qipan1 vinzheng kumar1.OLD qirli visheskumar kunli qirwu vissharma kuraj qxiong vivlam kuzhong raagarwal viyee kveeramah rabasu vjana kvshah rachatterjee vjishah kwahlin rachatterjee.OLD vkale kwwalton rachowdhury vkhanikaeva kwyu raclam vkodumurumee kwyyoo radsrinivasa vkondipati kyadav raggarg vkootagaram kychao ragte vlloyd kyethiraj rahhuang vloganathan kylanglois rahraja vlokwani kymjames raich vmaurya kyumin raiislam vmontanez kzzhang rairahman vpakala lahess rajatkumar vpamula lawlin rajdas vperkowski lbai ramhuang vranjan lbozarth ramorosso vratnala lcaradonna rannadi vrustagi lchi rapeaning vseecharan lchrastecka rashanbhag vsnu lcolleyndeso rashizawa vstaub lcooke ratwi vtangirala ldavalosalva raychen2 vvadia ldgraham rbaheti vvedanair lecheung rbasharat vvsharma ledong rbertolini wadawydiak ledwan rbhal waluo lee104 rbhansali wang110 lee111 rbhowmik wang113 lee75 rbiondo wang132 lehhou rbird wang148 leichen3 rbirnbaum wang154 leili1 rbodenstein wang159 leipan rboseroy wang54 leizhou rbronstein wang84 leprentis rburgert wangzhang leriksson rcconley wawen lernunez rchabot wayou lessig rckline wazzhang lesyan rcrizzo wbrett letucker rcsingh wcun lgruenburg rdavuluri wcunningham lhinners rdefrancisco wdaniels lhthorne rdhaipule wecui li1 rdhawan weibhuang li20 rdhillon weicdeng li3 rdogra weichang li32 rdrocha weichang.OLD liangzhu rdrucker weicheng liannchen rediaz weihong lichen8 refem weihsu lichiang relkin weihwang lifwang relyu weili3 lihahuang renunez weipeng lihazhang rfkelly weishen lihexu rflood weishi2 lihnguyen rflorek weiszhong lin56 rfrisina weitan linchen3 rgadi weituchen lincyu rgaonkar weizhu lingjpan rgautam welliao lingyang rgiles wenblu linjjiang rgmillard wenbwang linxu rgonzalez wendazhang linyi rgzhang wendhu lirzheng rhande wendu liszheng rharrison wendyang liu36 rhelbock wenhgao liu61 rherman wenjihuang liuwang rhesler wensliu liuyang2 rhoffren wentawu liuyzhou rhua wequ liwyang richatterjee whiwong ljescobar richkim wholt lkarpuskasan richlin wihu lkassetti rijayaraman withomas lko rikaur wiwang lkrug rikeh wixiang llevack riraquib wjchen llingda risjain wknop lmadiraju rispatil wlancer lmaeba ritagarwal wlian lmanathungam riwu wmichael lmconnolly rizhuang woaks lmdeoliveira rjayaramared wriggs lmunad rjbrowne wsander lnazarov rjdesmond wsanderson lnie rjeyachandra wshih lnolasco rjhuang wsuttle lonhan rjleung wthornton lorlowski rjsoni wweaver loswanson rjwillett wweiqiao lpanwang rkhanal xbarron lparrillamon rkhatwani xdmod lpbui rkhot xiachu lpei rkidambi xiamu lpintodealme rkoots xianaliu lprowant rkyatham xiangyuhuang lraguette rlarsen xiangyyang lrastelli rlpersaud xiaocao lrole rlsiford xiaodliu lsaleh rmakheja xiaogli lscampbell rmalga xiaohawang lschappell rmandloi xiaohuliu lschutz rmangalampal xiaokzhao lshekhar rmanku xiaoleyang lstrey rmatsibekker xiaolhu ltalbot rmax xiaolhuang ltngo rmenezes xiaolucheng ltorpey rmoffitt xiaotiawang ltorrehealy rmohan xiaotoli luge rmudhuganti xiaoxyang lujjia rmuthu xiaoysun luoshi rnarvekar xiaoyuli lusu rnorthrup xiaoyuyang luzou rochandramoh xicao lvasanthakum rodtan xichen10 lverma roessig xinachen lvotapka rohshukla xingma lwollmuth romjohnson xingtzhou lwreid ronassar xingyichen lyohe ronwang xingywang lyrodrigues root xingzguo maaibrahim rorosenberg xinhahuang maalynch roshukla xinlu2 maamandola roychen1 xinqian mabruzzeseot rparsons xintang madambrosio rpatanwadia xinwang2 madkar rpatro xinwang5 madowling rpatwary xinxu4 maedelmann rperna xinyazheng maescobarrod rpghosh xinyin maggchen rpmchugh xiulzhang maggonzalezg rpohankar xiwhuang maghazahedi rpopper xixxiong magmarkowska rraghunathan xizhang1 maguevarra rrani xji mahahn rristowhadli xjiao mahhasan rritu xqliu mahiralam rsamulyak xsha maiyedun rsandhu xshuqian makhdhor rsarker xuaqi makinboade rsejour xuaxu makmalone rsher xudeng makowalchyk rshilkrot xuebwang maksen rshimogawa xueqli maliyari rsihag xuxie malvin rsison xyuan mamahzabin rsmolinski yaagarwal mamandola rsoori yakang mamlan rspowers yang28 maochoa rstusalitus yang34 mapak rtamarkin yangfwu mapang rtelikicherl yangli10 marif rthacker yangli9 marioreyes rtrybulski yanglu2 markhangelsk ruhipatel yangxie markong ruicxu yangzhang masharma ruiding yangzhou masong ruihechen yanwang2 matique ruiqiwang yaoli2 matjones ruishi yaozou mattchang rulliu yashu mavanalstine runcli yaspatel mawwa ruossun yaxuan maxmuller ruparekh yazadeh mazhao rusharma yazou mazzimontire ruyu ybajaj mbandham rwales ychao mbarbosa rwilson yding mbastan rxli yehu mbender ryachen yejikim3 mbianchi ryanglee yeke mbliss ryao yellaham mboisvert rycchan yenwchen mbolko rychin yenwechen mborczuk ryengel yeonskang mbowen rygeorge yhannun mbozok rysalernoeic yhasib mbrunger rzlin yhochberg mbuskirk saachowdhury yibqi mcaponegro saaikhan yichuang mcfoley sabedin yiclin mchio sabergman yicozhu mcirrito sabeykoon yidcheng mckoch sabousamra yifagao mclim saconstantin yifasun mcng sadas yifewu mconners sadeshpande yigao2 mdabhole sadsharma yihanwang mdarita saerkim yihsu mdatar saffan yihua mdavariesfah sagchandrash yijiang3 mdeisler saichowdhury yijing mdelasaysork saihaque yijliu mdhuang saismail yijtian mdovedytis sakader yijzhu mdsweeney sakhalifa yiliu4 mdwalam sakinney yilma meemcnamara sakotagiri yimzhao meijli samachen yimzhu meisanchezpe samesingh yingczhou meisong samhoque yingfan meliasi samichowdhur yinglu1 meliot samrosner yinou memendi samung yinxzhang mempark samvasquez yinyou menalam sangyoon yipli menchowdhury sarani yiqguo mengao sasaluja yittian mengjliu sashrestha yiwasaki menglin1 sasnyder yiwchao mengrzhang sastephens yixcui mengtliu sasurana yiyayu mengwu saswang yiyizhou mengxwang satsaha yizholi mesch saukumar yjetwani meserranosos saupaul ykakade meyasmin saursingh ykhaliqui meyue savargas ykuyu mezaman saysharma ymaung mfbugallo sazchowdhury ymondal mferdman sbadlia yneelam mfierek sbaines yohe mfirmansyah sbajjuri yokato mfite sbanam yokee mforslund sbatheja yoki mfoydl sbeesabathun yomma mfucci sbeg yongjzhang mgarciadiaz sbenz yongmchoi mgcortes sbhuma yongshin mghaderibane sbillah yonxiang mghogale sbinnamangal yoshen mgholamianji sbire youcha mgivehki sbirrer youngkwon mgwhite sboddeti younkang mhanubal sboppudi yousshin mhare sbrahmadevar ypichkar mhaziz sbscott yrhamatzada mhijikata sburgert ysingh mhorowitz scberg ysoh mhott scduppala yson miachristie scentorrino ysoroka miahe schheda ytham mianchen schiappone yuanjchen mibbowman schook yuanzhao michaliang scokro yuasong michelhuang scsteiger yuchen4 michellhuang sdedhia yuchen7 michhuang sdefaz yuchzhou micnicolette sdescalso yucma micxu sdhalleweyn yucpu miczhao sdisalvo yucsun miduan sdivilov yucxing mignatov sdsouza yucye mihur sdssingh yudding mijia sebramirezvi yudichen mijrivera seg yuechen4 milobi seojchang yuefandeng miloska seongan yuehuang mimak seonghjeong yuejin minghazhang seongioh yuewang6 mingsun seshin yuewang7 mingyli sestoller yuewlin mingyzhang seunchoi yuezhao2 minhwang sexia yufchen minkwan sfardeen yuhajiang miray sfarhat yuhwu mireza sfarnan yulma miswong sfinch yuluwang mjadhav sfiola yulyu mjavanmard sfluo yumichen mjbonney sgajjala yunhxu mjchun sgala yunjeon mkaltak sgenovese yunlzhang mkamiya sghavamnia yunpan mkanasani sghavat yupeng mkanasani.OLD sgholami yuqianwu mkapadia sghorashi yuqiao mkaribian sgopalan yushuang mkhemchandan sgoswami yusjin mkishore sgrao yuttian mkochert sgrieninger yuwang7 mkoga sgurram yuwzhang mkondeti sguru yuxia4 mkonovalyuk sgwilliams yuxlin mkoraiem sgyuho yuxuanzhang mkpatel shaamin yuxushi mkritzer shakislam yuxwu mksanda shalirou yuyguo mkurakula shanhe yuzhwang mlaul shanlin2 yyokoi mlauterbur shaoliu zafahmad mlcollier shaowang zalseika mlng shaqin zariahmed mlondoo sharinarayan zballard mloverde shawmathew zbhinderwala mmadeira shcchakrabor zcheslog mmahboob shclay zcytryn mmahim shdesai zdoora mmaitra shdixit zdowling mmakeev shdixit.OLD zdupont mmarder shechoi zexizhang mmaskaliova shengzhu zeyao mmasoumi shengzwang zezhu mmatero shenjin zfallon mmaung sheshao zgrandison mmcduffie shexiong zgungor mmcneill shikgupta zhacai mmerenstein shilgupta zhage mmilhaven shilliu zhagu mmimurphy shiltian zhang100 mmursheed shitsai zhang110 mniznikiewic shivansharma zhang118 mnovotny shivgupta zhang123 moamin shiyuawang zhang133 mobusan shkhalid zhang142 moewilliams shmmohammed zhang152 moflus shmondal zhang173 mogao shopatel zhanyang mogoel shperalta zhaoliu mohassan shrajput zhchai mojia shroy zhddong molssi000 shrraman zhedzhang molssi001 shsaha zhefang molssi002 shshekhar zheng13 molssi003 shshekhar.OLD zheng30 molssi004 shsin zhengxwang molssi005 shssridhar zhenjhuang molssi006 shtao zhenliu molssi007 shuaguo zhenlu molssi008 shubwang zhenqian molssi009 shuhe zhenwu molssi010 shujia zhenxliu molssi011 shyyoo zheychen molssi012 shyyuan zhezhou1 molssi013 shzzhou zhibwang molssi014 siasun zhibyang molssi015 sichchen zhideng molssi016 sicheliu zhihhe molssi017 sichhabra zhihhuang molssi018 sichliu zhijli molssi019 sigadkar zhimalin molssi020 siggupta zhipxu molssi021 sihqian zhiwlin molssi022 sijhuang zhixzhang molssi023 sijjiang zhiye molssi024 sijliu zhke molssi025 silai zhlee molssi026 singanne zhonliang molssi027 singh4 zhouyu1 molssi028 sinhong zhuhli molssi029 sinlin zhuxie molssi030 sinsmith zhwong molssi031 sirle zhxia molssi032 sishizawa zidiao molssi033 siskhakov ziguan molssi034 siuchan zijiao molssi035 siwewang zijizhou molssi036 sixliu zikhan molssi037 siyadav zilinchen molssi038 siyao zilwu molssi039 siyimaya zirliu morahimi siyzou zishao moriasaranib sizahid ziweiwang mozhao sizzheng ziwyu mperess sjaffary zixli mpersch sjamshad ziyli mpetrusky sjeevan ziyozhang mpkatz sjens ziyye mpsantomauro sjiecheng zkrayem mquispecarba sjnelson zlyu mradfar sjyang zmou mrahimibolda skade zniu mrakhar skagana zoanderson mrashid skalam zoxie mrathore skalva zqiao mrayeesuddin skann zsongzhu mrehan skapse zuzheng mreuter skapur zwray mrichter skarnik zye mrius skatariya zzaidi mrkumar skavuri zzhuang mrosati sketchum zzoya mrsun skobayashi msardis skogilathota gpfs]$ cd projects/AMS536 junk.txt zzz.programs get_anchors.py zzz.anchors AMS536]$ cd zzz.programs/ zzz.programs]$ ls dock6-master.zip plot_footprint_single_magnitude.py dock_directory_arch plot_rmsds_amber gen-frags-12 VS_libraries zzz.programs]$ cd dock6.12_ams536/ dock6.12_ams536]$ ls README.md template_pipeline tutorials dock6.12_ams536]$ cd parameters/ parameters]$ ls fraglib_linker.mol2 prot.table.ambcrg.sybH fraglib_scaffold.mol2 sa_fraglib.dat fraglib_sidechain.mol2 screen.in fraglib_torenv.dat screen.para vdw_AMBER_parm94.defn na.table.ambcrg vdw_AMBER_parm94.dock3_7.defn pains_table_2019_09_01.dat vdw_AMBER_parm94.dock3_7_one_C_3.defn pains_table.dat vdw_AMBER_parm96.defn vdw_AMBER_parm99.defn prot.table.ambcrg.ambH vdw_de_novo.defn prot.table.ambcrg.pdb3H vdw.parms.amb prot.table.ambcrg.pdbH vdw.parms.update.amb parameters]$ pwd grams/dock6.12_ams536/parameters parameters]$ class AMS_536]$ cd Tutorials/5EEN/004_energymin/ 004_energymin]$ vi min.in 004_energymin]$ touch max.in 004_energymin]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/ dock6.12_ams536]$ ls README.md template_pipeline tutorials dock6.12_ams536]$ cd bin/ multigrid_fp_gen.py sevsolv nchemgrid_GB showbox nchemgrid_SA showsphere solvgrid solvmap prepare_amber.pl sphere_selector prepare_rna_amber.pl sphgen prepgen teLeap resp tleap respgen grams/dock6.12_ams536/bin AMS_536]$ cd Tutorials/5EEN/ 5EEN]$ cd 004_energymin/ 004_energymin]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i max.in

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Molecule Library Input Parameters

                                            ligand_atom_file [database.mol2] ():../001.structure/2ITO_ligand_Gefitinib_final.mol2
                                           limit_max_ligands [no] (yes no):
                                               skip_molecule [no] (yes no):
                                          read_mol_solvation [no] (yes no):
                                              calculate_rmsd [no] (yes no):yes
                                      use_rmsd_reference_mol [no] (yes no):yes
                                     rmsd_reference_filename [ligand_rmsd.mol2] ():../001.structure/2ITO_ligand_Gefitinib_final.mol2

Database Filter Parameters

                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):no

Bump Filter Parameters

                                                 bump_filter [no] (yes no):

Master Score Parameters

                                             score_molecules [yes] (yes no):

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):
                                    grid_score_rep_rad_scale [1] ():
                                        grid_score_vdw_scale [1] ():
                                         grid_score_es_scale [1] ():
                                         grid_lig_efficiency [no] (yes no):
                                      grid_score_grid_prefix [grid] ():../003_gridbox/grid

GIST Score Parameters

MultiGrid Score Parameters

Dock3.5 Score Parameters

Continuous Energy Score Parameters

Footprint Similarity Score Parameters

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

                                             minimize_ligand [yes] (yes no):
                                      simplex_max_iterations [1000] ():
                              simplex_tors_premin_iterations [0] ():
                                          simplex_max_cycles [1] ():
                                      simplex_score_converge [0.1] ():
                                      simplex_cycle_converge [1.0] ():
                                          simplex_trans_step [1.0] ():
                                            simplex_rot_step [0.1] ():
                                           simplex_tors_step [10.0] ():
                                           simplex_final_min [no] (yes no):
                                         simplex_random_seed [0] ():
                                       simplex_restraint_min [no] (yes no):yes
                               simplex_coefficient_restraint [10.0] ():

Atom Typing Parameters

                                                  atom_model [all] (all | united):
                                               vdw_defn_file [vdw.defn] ():
                                              flex_defn_file [flex.defn] ():
                                             flex_drive_file [flex_drive.tbl] ():

Molecule Library Output Parameters

                                       ligand_outfile_prefix [output] ():
                                         write_mol_solvation [no] (yes no):
                                          write_orientations [no] (yes no):
                                       num_scored_conformers [1] ():
                                             score_threshold [100.0] ():
                                                rank_ligands [no] (yes no):

Could not open vdw.defn for reading. Program will terminate.

(base) [ehspector@milan1 004_energymin]$ vimdiff min.in max.in 2 files to edit (base) [ehspector@milan1 004_energymin]$ rm max.in (base) [ehspector@milan1 004_energymin]$ vi min.sh (base) [ehspector@milan1 004_energymin]$ vi min.in (base) [ehspector@milan1 004_energymin]$ bash min.sh (base) [ehspector@milan1 004_energymin]$ ls 5een.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan1 004_energymin]$ vi min.out (base) [ehspector@milan1 004_energymin]$ ls 5een.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan1 004_energymin]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ ls 1086 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1086 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ mv 1086/ 1O86 (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 1O86/commands.txt (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ ls commands.txt (base) [ehspector@milan2 1O86]$ bash commands.txt (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore

 [Bookmarked Feb 7, 2025 at 3:22:42 PM]

(base) [ehspector@milan2 1O86]$ mv 004_dock/ 004_energymin (base) [ehspector@milan2 1O86]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls (base) [ehspector@milan2 001_structure]$ ls 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2 (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls (base) [ehspector@milan2 002_surface_spheres]$ ls 1O86_surface.dms (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 5EEN/ (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 5EEN]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 5een.sph 5een_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/sphere.sph 1O86/002_surface_spheres/sphere.sph (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 1O86/002_surface_spheres/select.sph (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/INSPH 1O86/002_surface_spheres/INSPH (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 1O86_surface.dms INSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph At line 131 of file sphgen.f (unit = 4) Fortran runtime error: Cannot open file '5een_surface.dms': No such file or directory

Error termination. Backtrace:

0 0x7ffff7d54ca5 in already_open

at ../../../libgfortran/io/open.c:742

1 0x404f73 in ???
2 0x40117c in ???
3 0x7ffff742958f in ???
4 0x7ffff742963f in ???
5 0x4011b4 in ???
6 0xffffffffffffffff in ???

(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ ls 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph At line 125 of file sphgen.f (unit = 6) Fortran runtime error: Cannot open file 'OUTSPH': File exists

Error termination. Backtrace:

0 0x7ffff7d54ca5 in already_open

at ../../../libgfortran/io/open.c:742

1 0x404e9e in ???
2 0x40117c in ???
3 0x7ffff742958f in ???
4 0x7ffff742963f in ???
5 0x4011b4 in ???
6 0xffffffffffffffff in ???

(base) [ehspector@milan2 002_surface_spheres]$ ls 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph At line 125 of file sphgen.f (unit = 6) Fortran runtime error: Cannot open file 'OUTSPH': File exists

Error termination. Backtrace:

0 0x7ffff7d54ca5 in already_open

at ../../../libgfortran/io/open.c:742

1 0x404e9e in ???
2 0x40117c in ???
3 0x7ffff742958f in ???
4 0x7ffff742963f in ???
5 0x4011b4 in ???
6 0xffffffffffffffff in ???

(base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph At line 125 of file sphgen.f (unit = 6) Fortran runtime error: Cannot open file 'OUTSPH': File exists

Error termination. Backtrace:

0 0x7ffff7d54ca5 in already_open

at ../../../libgfortran/io/open.c:742

1 0x404e9e in ???
2 0x40117c in ???
3 0x7ffff742958f in ???
4 0x7ffff742963f in ???
5 0x4011b4 in ???
6 0xffffffffffffffff in ???

(base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ vi 1086_new_surface.dms (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ vi sphere (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86_surface.dms INSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86.sph 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86.sph 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 1O86]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2 (base) [ehspector@milan2 001_structure]$ ls 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2 (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ bash select.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86_surface.dms OUTSPH select.sph 1O86.sph INSPH selected_spheres.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ ls 1086_new_surface.dms 1O86_surface.dms OUTSPH select.sph 1O86.sph INSPH selected_spheres.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.sh 1O86/003_gridbox/showbox.sh (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.in 1O86/003_gridbox/showbox.in (base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ vi showbox.sh (base) [ehspector@milan2 003_gridbox]$ bash showbox.sh (base) [ehspector@milan2 003_gridbox]$ ls

1O86.box.pdb   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.sh 1O86/003_gridbox/grid.sh (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.in 1O86/003_gridbox/grid.in (base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls

1O86.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan2 003_gridbox]$ vi grid. (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 1O86]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2 (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 1O86]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ bash grid.sh (base) [ehspector@milan2 003_gridbox]$ ls

1O86.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan2 003_gridbox]$ vi grid.out (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ bash grid.sh (base) [ehspector@milan2 003_gridbox]$ ls

1O86.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
grid.bmp       grid.nrg   grid.sh   '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 1O86/004_energymin/min.sh (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 1O86/004_energymin/min.in (base) [ehspector@milan2 Tutorials]$ cd 1O86/004_energymin/ (base) [ehspector@milan2 004_energymin]$ vi min.in (base) [ehspector@milan2 004_energymin]$ cd ../001_structure/ (base) [ehspector@milan2 001_structure]$ ls 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2 (base) [ehspector@milan2 001_structure]$ cd ../004_energymin/ (base) [ehspector@milan2 004_energymin]$ ls min.in min.sh (base) [ehspector@milan2 004_energymin]$ bash min.sh (base) [ehspector@milan2 004_energymin]$ ls 1O86.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan2 004_energymin]$ vi min.out (base) [ehspector@milan2 004_energymin]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 2w26]$ cd 001_structure/ (base) [ehspector@milan2 001_structure]$ ls (base) [ehspector@milan2 001_structure]$ cd .. (base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_surface.dms INSPH sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph At line 328 of file sphgen.f Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:

0 0x7ffff7d59e39 in formatted_transfer_scalar_read

at ../../../libgfortran/io/transfer.c:1790

1 0x7ffff7d5b535 in formatted_transfer

at ../../../libgfortran/io/transfer.c:2491

2 0x4049e0 in ???
3 0x40516a in ???
4 0x40117c in ???
5 0x7ffff742958f in ???
6 0x7ffff742963f in ???
7 0x4011b4 in ???
8 0xffffffffffffffff in ???

(base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_surface.dms (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_surface.dms INSPH OUTSPH sphere.sph temp1.ms temp3.atc (base) [ehspector@milan2 002_surface_spheres]$ rm temp1.ms (base) [ehspector@milan2 002_surface_spheres]$ rm temp3.atc (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26_surface.dms INSPH sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26.sph 2w26_surface.dms INSPH OUTSPH sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 2w26/002_surface_spheres/select.sph (base) [ehspector@milan2 Tutorials]$ cd 2w26/002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26.sph 2w26_surface.dms INSPH OUTSPH select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ cd ../001_structure/ (base) [ehspector@milan2 001_structure]$ ls 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2 (base) [ehspector@milan2 001_structure]$ cd ../002_surface_spheres/ (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph (base) [ehspector@milan2 002_surface_spheres]$ bash select.sph (base) [ehspector@milan2 002_surface_spheres]$ ls 2w26.sph 2w26_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph (base) [ehspector@milan2 002_surface_spheres]$ cd .. (base) [ehspector@milan2 2w26]$ cd 003_gridbox/ (base) [ehspector@milan2 003_gridbox]$ ls

grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan2 003_gridbox]$ rm '&showbox.log&' (base) [ehspector@milan2 003_gridbox]$ ls grid.in grid.sh showbox.in showbox.sh (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ vi showbox.sh (base) [ehspector@milan2 003_gridbox]$ vi showbox.in (base) [ehspector@milan2 003_gridbox]$ bash showbox.sh (base) [ehspector@milan2 003_gridbox]$ ls

2w26.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh

(base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ vi grid.in (base) [ehspector@milan2 003_gridbox]$ vi grid.sh (base) [ehspector@milan2 003_gridbox]$ bash grid.sh (base) [ehspector@milan2 003_gridbox]$ ls

2w26.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
grid.bmp       grid.nrg   grid.sh   '&showbox.log&'

(base) [ehspector@milan2 003_gridbox]$ vi grid.out (base) [ehspector@milan2 003_gridbox]$ cd .. (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 2w26]$ vi commands.txt (base) [ehspector@milan2 2w26]$ mv 004_dock/ 004_energymin (base) [ehspector@milan2 2w26]$ cd 004_energymin/ (base) [ehspector@milan2 004_energymin]$ ls (base) [ehspector@milan2 004_energymin]$ ls (base) [ehspector@milan2 004_energymin]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 2w26/004_energymin/min.in (base) [ehspector@milan2 Tutorials]$ cd 2w26/004_energymin/ (base) [ehspector@milan2 004_energymin]$ vi min.in (base) [ehspector@milan2 004_energymin]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 2w26/004_energymin/min.sh (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan2 2w26]$ cd 004_energymin/ (base) [ehspector@milan2 004_energymin]$ vi min.sh (base) [ehspector@milan2 004_energymin]$ bash min.sh (base) [ehspector@milan2 004_energymin]$ ls 2w26.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan2 004_energymin]$ vi min.out (base) [ehspector@milan2 004_energymin]$ client_loop: send disconnect: Broken pipe (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 5een.sph 5een_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ vi select.sph (base) [ehspector@milan1 002_surface_spheres]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ home (base) [ehspector@milan1 espector]$ cd 4s0v/ (base) [ehspector@milan1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@milan1 4s0v]$ cd gas_teiger/ (base) [ehspector@milan1 gas_teiger]$ ls gas_2.in gas_3.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2 gas_2.out gas.in no_charge no_gas.out_scored.mol2 gas_3.in gas.out no_gas.in test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in (base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@milan1 gas_teiger]$ ls gas_2.in gas_3.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2 gas_2.out gas.in no_charge no_gas.out_scored.mol2 gas_3.in gas.out no_gas.in test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas_2.out (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in (base) [ehspector@milan1 gas_teiger]$ vi test_mol2 (base) [ehspector@milan1 gas_teiger]$ vi test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2 (base) [ehspector@milan1 gas_teiger]$ cd ../../builds/alpha_branch/src/dock (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ home (base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@milan1 gas_teiger]$ pwd /gpfs/projects/rizzo/espector/4s0v/gas_teiger (base) [ehspector@milan1 gas_teiger]$ cp gas_2.in gas_4.in (base) [ehspector@milan1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_2.out gas_4.in gas.out_scored.mol2 no_gas.out test_nocharge.mol2 1AAQ_yesG.mol2 gas_3.in gas.in no_charge no_gas.out_scored.mol2 gas_2.in gas_3.out gas.out no_gas.in test.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas_4.in (base) [ehspector@milan1 gas_teiger]$ vi gas_4.in (base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 gas_teiger]$ vi gas_4.out (base) [ehspector@milan1 gas_teiger]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ cd 5EEN/ (base) [ehspector@milan1 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/ (base) [ehspector@milan1 002_surface_spheres]$ ls 5een.sph 5een_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph (base) [ehspector@milan1 002_surface_spheres]$ vi select.sph (base) [ehspector@milan1 002_surface_spheres]$ home (base) [ehspector@milan1 espector]$ cd .. (base) [ehspector@milan1 rizzo]$ home (base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@milan1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_2.out gas_4.in gas.out no_gas.in test.mol2 1AAQ_yesG.mol2 gas_3.in gas_4.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2 gas_2.in gas_3.out gas.in no_charge no_gas.out_scored.mol2 (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 gas_teiger]$ rm gas_4.out (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 gas_teiger]$ vi gas_4.out (base) [ehspector@milan1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_2.out gas_4.in gas.out no_gas.in test.mol2 1AAQ_yesG.mol2 gas_3.in gas_4.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2 gas_2.in gas_3.out gas.in no_charge no_gas.out_scored.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas_4.in (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_2.out gas_4.in gas.in no_charge no_gas.out_scored.mol2 1AAQ_yesG.mol2 gas_3.in gas_4.out gas.out no_gas.in test.mol2 gas_2.in gas_3.out gas_4.out_scored.mol2 gas.out_scored.mol2 no_gas.out test_nocharge.mol2 (base) [ehspector@milan1 gas_teiger]$ vi gas_4.out_scored.mol2 (base) [ehspector@milan1 gas_teiger]$ cp gas_4.in gas_5.in (base) [ehspector@milan1 gas_teiger]$ vi gas_5.in (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_5.in -o gas_5.out (base) [ehspector@milan1 gas_teiger]$ vi gas_5.out (base) [ehspector@milan1 gas_teiger]$ home (base) [ehspector@milan1 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi rdtyper.cpp (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ cd .. (base) [ehspector@milan1 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@milan1 src]$ cd dock (base) [ehspector@milan1 dock]$ ls amber_typer.cpp filter.o mem_info.h score_internal.cpp amber_typer.h fingerprint.cpp mem_info.o score_internal.h amber_typer.o fingerprint.h nab score_internal.o base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp base_grid.h fraggraph.cpp nab.h score_multigrid.h base_grid.o fraggraph.h orient.cpp score_multigrid.o base_mpi.cpp fraggraph.o orient.h score.o base_mpi.h fragment.cpp orient.o score_ph4.cpp base_mpi.o fragment.h rddrive.cpp score_ph4.h base_score.cpp fragment.o rddrive.h score_ph4.o base_score.h gasteiger.cpp rddrive.o score_sasa.cpp base_score.o gasteiger.h rdtyper.cpp score_sasa.h conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp conf_gen_ag.o grid.h README score_solvent.h conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o conf_gen_cg.h gzstream sasa.h score_volume.cpp conf_gen_cg.o hungarian.cpp sasa.o score_volume.h conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h conf_gen_ga.cpp library_file.h score.cpp sphere.o conf_gen_ga.h library_file.o score_descriptor.cpp tnt conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl conf_gen_hdb.o lol score_footprint.h trace.o defreal.h Makefile score_footprint.o utils.cpp dock.cpp master_conf.cpp score_gist.cpp utils.h dockmol.cpp master_conf.h score_gist.h utils.o dockmol.h master_conf.o score_gist.o version.h dockmol.o master_score.cpp score.h xlogp.cpp dock.o master_score.h score_hbond.cpp xlogp.h filter.cpp master_score.o score_hbond.h filter.h mem_info.cpp score_hbond.o (base) [ehspector@milan1 dock]$ cd .. (base) [ehspector@milan1 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@milan1 src]$ cd .. (base) [ehspector@milan1 alpha_branch]$ ks -bash: ks: command not found (base) [ehspector@milan1 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@milan1 alpha_branch]$ cd src/ (base) [ehspector@milan1 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@milan1 src]$ cd .. (base) [ehspector@milan1 alpha_branch]$ cd install/ (base) [ehspector@milan1 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@milan1 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 10 01:24:01 PM EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fingerprint.h:13,
                from fingerprint.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fingerprint.h:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fraggraph.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fraggraph.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fragment.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from gasteiger.h:8,
                from gasteiger.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from gasteiger.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from hungarian.h:7,
                from hungarian.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from hungarian.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from library_file.h:9,
                from library_file.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from library_file.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from limit_max_change.h:12,
                from limit_max_change.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from limit_max_change.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from master_conf.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from master_conf.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from master_score.cpp:2:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from master_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

^Cmake[1]: *** [../../install/rules.h:36: master_score.o] Interrupt make: *** [Makefile:28: dock] Interrupt

(base) [ehspector@milan1 install]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Permission denied, please try again. ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

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Pushed a login request to your device... Success. Logging you in... (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 10 13:29:04 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

^Cmake[1]: *** [conf_gen_ag.o] Interrupt make: *** [dock] Interrupt

(base) [ehspector@login2 install]$ rdkit bash: rdkit: command not found... (base) [ehspector@login2 install]$ rd srun: error: invalid partition specified: short-40core srun: error: Unable to allocate resources: Invalid partition name specified (base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ rd srun: job 925032 queued and waiting for resources srun: job 925032 has been allocated resources (base) [ehspector@dn018 ~]$ home (base) [ehspector@dn018 espector]$ cd builds/alpha_branch/install/ (base) [ehspector@dn018 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn018 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 10 13:31:12 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fingerprint.h:13,
                from fingerprint.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fingerprint.h:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fraggraph.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fraggraph.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fragment.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from gasteiger.h:8,
                from gasteiger.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from gasteiger.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from hungarian.h:7,
                from hungarian.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from hungarian.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from library_file.h:9,
                from library_file.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from library_file.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from limit_max_change.h:12,
                from limit_max_change.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from limit_max_change.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from master_conf.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from master_conf.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from master_score.cpp:2:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from master_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from orient.h:7,
                from orient.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from orient.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from sasa.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from sasa.h:14:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_amber.cpp:66:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_amber.cpp:55:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_chemgrid.cpp:39:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_chemgrid.cpp:38:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_descriptor.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_descriptor.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_footprint.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_footprint.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_ph4.h:7,
                from score_ph4.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_ph4.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_volume.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_volume.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_gist.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_gist.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_hbond.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_hbond.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_internal.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_internal.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_multigrid.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_multigrid.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_sasa.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_sasa.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_solvent.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_solvent.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from simplex.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from simplex.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from utils.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from utils.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.h:12,
                from iso_align.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fragment.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
                from rdtyper.cpp:18:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from rdtyper.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from rddrive.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from dockmol.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

cd nab && make all make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs mv dock6.rdkit ../../bin make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Mon Feb 10 13:34:18 EST 2025.

(base) [ehspector@dn018 install]$ exit exit (base) [ehspector@milan1 ~]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ home (base) [ehspector@milan1 espector]$ cd .. (base) [ehspector@milan1 rizzo]$ module load git (base) [ehspector@milan1 rizzo]$ home (base) [ehspector@milan1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan1 espector]$ git status fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). (base) [ehspector@milan1 espector]$ cd builds/ (base) [ehspector@milan1 builds]$ cd alpha_branch/ (base) [ehspector@milan1 alpha_branch]$ git status On branch alpha_branch Your branch is up to date with 'origin/alpha_branch'.

Changes not staged for commit:

 (use "git add <file>..." to update what will be committed)
 (use "git restore <file>..." to discard changes in working directory)

modified: docs/new_in_6.13.txt modified: src/dock/filter.cpp

Untracked files:

 (use "git add <file>..." to include in what will be committed)

src/dock/lol src/rdkit/boost/ src/rdkit/boost_1_71_0.tar.gz src/rdkit/boost_1_71_0/ src/rdkit/eigen-3.3.9.tar.gz src/rdkit/eigen-3.3.9/ src/rdkit/rdkit-Release_2019_09_1.tar.gz src/rdkit/rdkit-Release_2019_09_1/

no changes added to commit (use "git add" and/or "git commit -a") (base) [ehspector@milan1 alpha_branch]$ git commit src/dock/filter.cpp Aborting commit due to empty commit message. (base) [ehspector@milan1 alpha_branch]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 005_virtual_screen/ (base) [ehspector@milan1 005_virtual_screen]$ ls (base) [ehspector@milan1 005_virtual_screen]$ cd .. (base) [ehspector@milan1 2w26]$ mv 005_virtual_screen/ 005_footprint/ (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_footprint 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 005_footprint/ (base) [ehspector@milan1 005_footprint]$ ls (base) [ehspector@milan1 005_footprint]$ touch footprint.in (base) [ehspector@milan1 005_footprint]$ ls footprint.in (base) [ehspector@milan1 005_footprint]$ cd .. (base) [ehspector@milan1 2w26]$ cd 004_energymin/ (base) [ehspector@milan1 004_energymin]$ ls 2w26.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan1 004_energymin]$ vi 2w26.lig.min_scored.mol2 (base) [ehspector@milan1 004_energymin]$ ls 2w26.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan1 004_energymin]$ vi min.s (base) [ehspector@milan1 004_energymin]$ vi min.sh (base) [ehspector@milan1 004_energymin]$ cd ../ (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_footprint 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ vi commands.txt (base) [ehspector@milan1 2w26]$ cd ,, -bash: cd: ,,: No such file or directory (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_footprint 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 005_footprint/ (base) [ehspector@milan1 005_footprint]$ ls footprint.in (base) [ehspector@milan1 005_footprint]$ mv footprint.in rigid.in (base) [ehspector@milan1 005_footprint]$ vi rigid.sh (base) [ehspector@milan1 005_footprint]$ cd .. (base) [ehspector@milan1 2w26]$ mv 005_footprint/ 005_rigid (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_rigid 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 005_rigid/ (base) [ehspector@milan1 005_rigid]$ ls rigid.in rigid.sh (base) [ehspector@milan1 005_rigid]$ bash rigid. bash: rigid.: No such file or directory (base) [ehspector@milan1 005_rigid]$ bash rigid.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Molecule Library Input Parameters

                                            ligand_atom_file [database.mol2] ():
                                           limit_max_ligands [no] (yes no):
                                               skip_molecule [no] (yes no):
                                          read_mol_solvation [no] (yes no):
                                              calculate_rmsd [no] (yes no):

Database Filter Parameters

                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):
                                          automated_matching [yes] (yes no):
                                          receptor_site_file [receptor.sph] ():
                                            max_orientations [1000] ():
                                             critical_points [no] (yes no):
                                           chemical_matching [no] (yes no):
                                          use_ligand_spheres [no] (yes no):

Bump Filter Parameters

                                                 bump_filter [no] (yes no):

Master Score Parameters

                                             score_molecules [yes] (yes no):

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):
                                    grid_score_rep_rad_scale [1] ():
                                        grid_score_vdw_scale [1] ():
                                         grid_score_es_scale [1] ():
                                         grid_lig_efficiency [no] (yes no):
                                      grid_score_grid_prefix [grid] ():

GIST Score Parameters

MultiGrid Score Parameters

Dock3.5 Score Parameters

Continuous Energy Score Parameters

Footprint Similarity Score Parameters

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

                                             minimize_ligand [yes] (yes no):
                                      simplex_max_iterations [1000] ():
                              simplex_tors_premin_iterations [0] ():
                                          simplex_max_cycles [1] ():
                                      simplex_score_converge [0.1] ():
                                      simplex_cycle_converge [1.0] ():
                                          simplex_trans_step [1.0] ():
                                            simplex_rot_step [0.1] ():
                                           simplex_tors_step [10.0] ():
                                           simplex_final_min [no] (yes no):
                                         simplex_random_seed [0] ():
                                       simplex_restraint_min [no] (yes no):

Atom Typing Parameters

                                                  atom_model [all] (all | united):
                                               vdw_defn_file [vdw.defn] ():
                                              flex_defn_file [flex.defn] ():
                                             flex_drive_file [flex_drive.tbl] ():

Molecule Library Output Parameters

                                       ligand_outfile_prefix [output] ():
                                         write_mol_solvation [no] (yes no):
                                          write_orientations [no] (yes no):
                                       num_scored_conformers [1] ():
                                             score_threshold [100.0] ():
                                                rank_ligands [no] (yes no):

Could not open vdw.defn for reading. Program will terminate.

(base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ rm rigid.in (base) [ehspector@milan1 005_rigid]$ touch rigid.in (base) [ehspector@milan1 005_rigid]$ ls rigid.in rigid.sh (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ bash rigid.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Molecule Library Input Parameters

                                            ligand_atom_file [database.mol2] ():2w26.lig.min.mol2
                                           limit_max_ligands [no] (yes no):
                                               skip_molecule [no] (yes no):
                                          read_mol_solvation [no] (yes no):
                                              calculate_rmsd [no] (yes no):yes
                                      use_rmsd_reference_mol [no] (yes no):yes
                                     rmsd_reference_filename [ligand_rmsd.mol2] ():2w26.lig.min.mol2

Database Filter Parameters

                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):  
                                          automated_matching [yes] (yes no):
                                          receptor_site_file [receptor.sph] ():../002_surface_spheres/selected_spheres.sph
                                            max_orientations [1000] ():
                                             critical_points [no] (yes no):
                                           chemical_matching [no] (yes no):
                                          use_ligand_spheres [no] (yes no):

Bump Filter Parameters

                                                 bump_filter [no] (yes no):

Master Score Parameters

                                             score_molecules [yes] (yes no):

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):
                                    grid_score_rep_rad_scale [1] ():
                                        grid_score_vdw_scale [1] ():
                                         grid_score_es_scale [1] ():
                                         grid_lig_efficiency [no] (yes no):
                                      grid_score_grid_prefix [grid] ():../003_gridbox/grid

GIST Score Parameters

MultiGrid Score Parameters

Dock3.5 Score Parameters

Continuous Energy Score Parameters

Footprint Similarity Score Parameters

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

                                             minimize_ligand [yes] (yes no):
                                      simplex_max_iterations [1000] ():
                              simplex_tors_premin_iterations [0] ():
                                          simplex_max_cycles [1] ():
                                      simplex_score_converge [0.1] ():
                                      simplex_cycle_converge [1.0] ():
                                          simplex_trans_step [1.0] ():
                                            simplex_rot_step [0.1] ():
                                           simplex_tors_step [10.0] ():
                                           simplex_final_min [no] (yes no):
                                         simplex_random_seed [0] ():
                                       simplex_restraint_min [no] (yes no):

Atom Typing Parameters

                                                  atom_model [all] (all | united):
                                               vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_AMBER_parm99.defn        
                                              flex_defn_file [flex.defn] ():
                                             flex_drive_file [flex_drive.tbl] ():

Molecule Library Output Parameters

                                       ligand_outfile_prefix [output] ():rigid.out
                                         write_mol_solvation [no] (yes no):
                                          write_orientations [no] (yes no):
                                       num_scored_conformers [1] ():
                                             score_threshold [100.0] ():
                                                rank_ligands [no] (yes no):

Could not open flex.defn for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn

Could not open flex_drive.tbl for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Initializing Library File Routines...

Could not open 2w26.lig.min.mol2 for reading. Program will terminate.

(base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ cp rigid.sh rigid_2.sh (base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh (base) [ehspector@milan1 005_rigid]$ ls rigid_2.sh rigid.in rigid.out rigid.sh (base) [ehspector@milan1 005_rigid]$ vi rigid.out (base) [ehspector@milan1 005_rigid]$ cd ../004_energymin/ (base) [ehspector@milan1 004_energymin]$ ls 2w26.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan1 004_energymin]$ cd ../005_rigid/ (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh (base) [ehspector@milan1 005_rigid]$ ls rigid_2.sh rigid.in rigid.out rigid.out_scored.mol2 rigid.sh (base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2 (base) [ehspector@milan1 005_rigid]$ vi rigid.out (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh (base) [ehspector@milan1 005_rigid]$ ls rigid_2.sh rigid.in rigid.out rigid.out_scored.mol2 rigid.sh (base) [ehspector@milan1 005_rigid]$ vi rigid.out (base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2 (base) [ehspector@milan1 005_rigid]$ cd .. (base) [ehspector@milan1 2w26]$ mv 006_virtual_screen_mpi/ 006_flex_docking (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_rigid 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_flex_docking 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 005_rigid/ (base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_rigid 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_flex_docking 008_rescore Notes.txt (base) [ehspector@milan1 2w26]$ cd 001_structure (base) [ehspector@milan1 001_structure]$ ls 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd .. (base) [ehspector@milan1 2w26]$ cd 005_rigid/ (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh (base) [ehspector@milan1 005_rigid]$ ls rigid_2.sh rigid.in rigid.out rigid.out_scored.mol2 rigid.sh (base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2 (base) [ehspector@milan1 005_rigid]$ vi rigid.out (base) [ehspector@milan1 005_rigid]$ vi rigid.in (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh (base) [ehspector@milan1 005_rigid]$ ls rigid_2.sh rigid.in rigid.out rigid.out_conformers.mol2 rigid.out_scored.mol2 rigid.sh (base) [ehspector@milan1 005_rigid]$ grep -c "Name" rigid.out_scored.mol2 7 (base) [ehspector@milan1 005_rigid]$ client_loop: send disconnect: Broken pipe (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan1 ~]$ cd AMS_536/ (base) [ehspector@milan1 AMS_536]$ ls class_project Tutorials (base) [ehspector@milan1 AMS_536]$ cd .. (base) [ehspector@milan1 ~]$ cd .. (base) [ehspector@milan1 home]$ ls caaachase dbobo jksullivan msazonova skorada aaaggarwal dcalabria jktsui mschedel skotelnikov aaaggarwal.26FEB2020 dcazorla jleehand mschrimpf skotla aabdurrob dcbrown jlfong mschwaller skrichevsky aabhilash dcharan jlguerra mshaaban skristam aadarsh dchien jlipshultz mshahneousba skrupp aadubois ddassanis jlomanto mshih sladerwager aagashe ddelayo jluceno mshinder slakshminara aagishtein ddemartini jlungu mshu slaverty aahern ddukes jlutsky msilfies slthomas aaiyer deachen jlweissman msmoawad smadishetty aajith decarlson jmaghakian msrao smaiti aakale dekblom jmarcantonio msreeves smallipattu aakiti delam jmarciano mstanacevic smamalis aakkumar demccabe jmayortorres msweber smartynenko aaksenova dereliu jmeliker mtalukder smascarenhas aaliang deroy jmendezmende mthu smconnors aallin devlin jmgentile mtoledorozyc smdick aallu dfarahmandpo jmiao mtsonev smedved aalpern dfei jmitchell mturk smeghdadizan aamahmood dfucich jmorkos mumarani smelhiraj aambrown dgaidhani jmulackal muprit smesiha aamgalan dgenet jmurrugarral mvalakonda smhenry aaminev dgersappe jmurzaku mvashishtha smiduthuri aamurthy dg-mgmt1-auth-keys jmvasquez mvfernandezs smilakovic aanaggarwal dg-mgmt2-auth-keys jnassar mvilensky smirghafouri aanagnostopo dgnatenko jnatarajan mwilking smirroshande aanik dgoon jnery myarif smofakham aaprasad dgruzdev jnicasio myearsley smui aarasappan dgursoy jnmauro myoungblood smukherjee aarefin dgwood jnong mysql smvaccaro aarmas dhailegeorgi joawilson mzamani snarmeen aarroyave dhamam jocai mzepedaaguil snigam aasim dhandzlik jocwilliams mzhang snikhil aaslov dhdesouza jodey naahassan snimatullo aates dhildreth jodoh nabchowdhury snizambad aaurora dhongyi jodweinstein nabsyed snolas aavadhani dhperumal joeleung nacchen snyman aavira dhualong joeychan nacharya soba aaydin diannace jofranklin nagnihotri sochakrabort aaysheth disandovalch johbernard nagutierrez sohshin ababbar diwliu johnliu nalewis sohtsuka abadhe djagnarain joifan nanqwang solhapark abahadori djgold jomyoung napopova somishra abaidya djlambert jonamartins naqiu somunoz aball djoh jonicholson nasweet sooapark abardizbania djulian jonsu natsai sopjang abbhaskar djyu jonyin nazzhou sortizbetanc abeahmad dkadams joolee nbalasubrama sosarangi abenslama dkharzeev joosuh nbasok sosuresh abialkowska dkirby joroiland nbayas sowu abjoshi dkozakov joshmathew nbodduluri sozturk abkanevsky dkunjadiya joshumartin nbosviel spaci abogetti dlanger jovvazquezri nbowers spandrekar aborad dlhe joying nciotoli spang aborcatasciu dlucksted jozhao ncmeloottu spapazahario aborger dmahalli jpantano ncpathak spapazis aborowicz dmahzabin jparise ndcertain sparvathredd abozin dmale jparkinson ndev spathrose abphilip dmarkov jpascal ndheilly spilkey abrady dmarr jpcastillo ndigrandi spiret absalem dmckinnon jperezrios ndnguyen splee abtambe dmirfenderes jpeshansky ndokania spochron aburford dmorenosanti jpitt ndurand spothumahant acage dmukherjee jpmoryl ndzikowski spriyadarsha acalder dmulbagalven jporavanthat nesteves spugach acali dnanjappa jpwhite nexposescan sqavi acamino dnimatullo jqxiao neyang srahmani acastiblanco dnterry jranjan nezheng sraisinghani accapua dobyrne jrawski nfaiza sramanarajan acchakravart dochoi jrcheung nfpugliese sramanarajan.OLD acherath dofu jrcorbett nganu sramjan achouhan dohhlee jrest nghoang sramstrom acmarra dokkang jrgorman ngitman srashidian adamare dongsong jrimel ngluck sretineni adanial dongwhan jrkamler ngujarati srgupte adanoji donshi jrleeman nhamdan srnalluri adharan dotan jrojahn nhirtle srpayne adiloreto doyjang jrutledge nichaturvedi srshende ading dozhong jrwei nidimeglio ssabaghian admannino dpadhorny jsaldivar nigreen ssagynbayeva adpeng dpare jsalley nileong ssandal adpollack dparedesmeri jsaltz niranmanesh ssarnot adrana dparwana jsaputo nisankar ssarwar adrflorio dpati jsaxena nisong sseepersaud adrogers dpatil jscanderson nisoni ssemerkant adubey dpenchoff jschuchart nivsingh sserbin adutt dpfennell jschwedes njschwartzap sshaharia aecuomo dpotemkin jseeliger nkahmed sshapourmian aeichert drendina jseol nkandru ssheikhi aeltareb drhamilton jsgordon nkatla sshoque aeweiss dschneble jsinanan nkdean sshrestha afahmed dseddoh jsistla nkeer sshrivastava afarhadzadeh dsforza jskowalski nkhalsa ssivalenka afgregory dshangase jslogan nkhandagale ssjohn afrigo dsingla jsmaers nkhatri sskiena afurey dsli jsmucker nkinalis ssomani agaffoor dslo jsteier nkinlock ssperrottet agaikwad dsmolarski jsuchan nkyose sstoller agarforth dstepanenko jtalaveragre nleak sstoyanov agargueta dstrenski jtekverk nlogozzo ssundar agauer dswesty jtepan nlrogers ssunia aghai dthanassi jtevans nmahamud ssyedfahad agilgomez dtpham jtgabrielli nmaher ssyritsyn agmaharaj dtsybychev jtjones nmanzella staralekar agnsinha dtung jtmessina nmarcella stawong agopalkrishn duwwang jtrelewicz nmathew stelehany agraikos dvahabli jtrue nmehanna sthaker agugel dvyas juaalcantara nmeister sthorgusen agulhane dwhitty juffeng nmenasche stjjiang ahalwah dwiczer julima nmendiratta stmandell ahc dwillcox juliwu nmeruva stmccabe ahmkhan dzavala jumma nmichielsen stomar ahomayounnik dziadlou junding nmitra stpak ahsingh eadas jungshwang nnadkarni strainer ahurtado earavera junholee nnaitlho ststern ahxiao eatkinson junhuzhang nnakka stuznik aicheng ebagherizade junhyelee nnawal stzeng aidnani ebartlett junjiang nnehaindrani stzou ailyu eboria junkang nnghiemvu sudkhan airussell ebreen junszhou nniemiec sukkumar ajacovelli ebremer juntyao noibrahim sunarasimhas ajalwan ebrini junwang5 nolconner sunarasimhas.OLD ajamieson ebryski junxialiu novsingh sunghucho ajasniew ecarcelespov junywang npahlavan sunkim2 ajchan ecgross jusandoval npanagodawet surmy ajchavez echurch juschan nparghi sushahid ajhong eclemmon jusliu npasari suwei ajkoller ecline jusong npayen svadnerkar ajlli ecoutsias justili npomata svaldez ajmasella ecowley jusu npregosin svanderpoel ajoung edeturk juychen nrajput svayasi ajscarlatos edma juyyan nramdin svee ajtran edowney juzou nreaton swaxman ajwelsh edzhang jvansnellenb nsalekfarama swchaudhury ajyadav eeryildiz jvaska nsampson swen akalugade efinson jverbaarscho nsehgal sweverma akanodia egebb jvishal nshouman swpaul akapote egentles jvpepe nsimakov sxchen akarkare egouvis jvu nsipperly syaddanapudi akarzai eheywood jwahhab nsmehta syalla akaufman ehspector jwcross nsoder syarma akhibovska ejcarey jwcusick nsokolow syatigala akhosronejad ejguan jwisdom nsomani syatskar akhoukhi ejli jwlodek nstreb sydiaz akingan ejohnfelt jxue ntadler syousef akirillov ekandov jyerrick ntardugno sytlee akkale ekbetancourt jyluo ntetrault tabhatia akonosky ekeck jzoodsma ntippabhatla tadoyle akravchuk ekeough kabichandani ntripti taeklee akrowe ekhew kadeng nvafaeinajaf taeyounkim aktyagi eklau kadiallo nvitek tagiles akucich ekoo kadill nvohra tahkhan akuduregundi elari kadreher nvsutherland tajjung akundhuru elettieri kafarber nwein takther akverma elgchan kaifzheng nwweber talama akwakye elharris kaili nxlee talare alabella eli kailiu2 nyfletcher talin alaing ellai kailjiang obellinson tallison alanhuang elleisenberg kaimxu odeshpande tamislam alchung elmlowe kaitong odiamond tanis aldong elogeswar kaixichen odickerson taryu aldraper elslattery kamhassan oeskiocak tbabu alehsu emacosta kamrivera ohaputhanthr tbertino alem emarants kanagarwal ohyejin tbrackins alexhernande emarkowitz kanzhao okim tbrinckmann alfwu emarzigliano kapatel okoren tbrinkley algrullon embriggs kaporter omcgranaghan tburfeind alhhuang emrlin kapu omorozova tbushra alianwar emroberts karamachandr omoy tcanli alicwang emyhand kargill onatu tchatterton alietzau enebet kasong oogunfolakan tchristy alifeng eoruro katalwar ooreilly tchugh aliguori eozkirimli katschmidt orambow tcotroneo alindquist epapadopoulo kbaylous osdeshpande tdawar allekim erandhawa kbdiaz oshakkour tdiprima allelin eraut kbeckerredd oshetty tdviri allwong erbraun kbelfon osteele tema almabraham erfan kberard oyang testro almishra erglukhov kberghaus oyasar tgavryshko alokre ericlin1 kccoughlin padari tglotch alowell erizhou kchetan paggarwal tgrgas alperezmendo erkumar kchitale pahan tgrossberndt alqin erluo kdas pallen tguttula alsli erosenberg kdavidson pamishra thamada alvhsu errjones kdehmelt parjain thausch alynegron erschroeder kdemir parmitage thdavidson amacinnis erwhuang kdevedzhiev patflanagan therault amaffei esahin kdhar patmuller therodrigues amanagarwal esalman kdhuri pavkirkar thollis amanpsingh esaraivanov kdyro pavnkaur thomlin amanzoor eschiltzrous kebui pawu thren amaresca eshaji keckartt payao thzhou amarya eshetreatkle kelam pb tianyuawang amassari eshih keliao pbaliga tili amasuno eshuryak kellywang pcascantebon timji ambbrown esicoli kelvlin pcastillo timshi amccumber esiegmann kenchin pchinthamred tinggao amcelroy esogut kenhu pdalaya tinghwu amchale esonmez kennwu pdamore tingliu2 amcpherran essingh kereid pdevarajan tingslin amehla eswong kerwood pdjuric tinliu amehmood etakeuchi kevazquez pdonat tiwwong amgondal etalis kevcai pdongle tixi amibrahim etchan kevcheng pdutta tiyuan amigues etcheung keviliu pechang tjarrett amisaha ethresher kevwei peihsieh tjohannessen amkgupta etmonaco kexi peinwang tkarwal amnoonan etrommer kfatema penzhang tknoll amohamed etsang kfernando pesun tkohlmann amohammadrez etwest kflora pferrero tkral amohanty etyen kfryer pgaikar tkurc amohideen evalin kgarg pganapathi tla amoonilal evaxie kgayadhankar pganesh tlata amrabet evergaracobo kgcassar pgodoy tloden amramroop evxie kgjonas pgoldbart tlonsway amrangwala ewpeterson kgoranta pgoriparthi tmcgee amritpsingh exiu kgulati pgubbala tmia amullhaupt eylei khajny pguo tmohandas amychen5 eyzhu khasegawa pgurung tmoriya amyla fabdinov khoh phariprasad tmsmyth anadelgado faliang khumphries phowlader tmuntean analekseenko falmodaresit khyunjae phtnguyen tnle anarora faluo kihan phyeh tnsingletary ancollins fang1 kim128 pinlee toneal andcheung fanliu2 kim169 pinliu toye andguo fannli kim65 pjgriffin tpalit andgutierrez fanwang1 kingle pkaelbling tqduong andrchu faoki kipoon pkayedpour tqle andrwu faslanbeigi kisrani pkidambi traj andylin2 fatrahman kissung pkottapalli trichen anearora fatsai kjamal pkrstic trli anegi faye kjayanettiar pkuan trosenlicht aneiman fayyang kjroberts pkwoczak tsclement anejoshi fbasharat kjtorres pliu tshrestha anejoshi.OLD fbischoff kjun plorenagodoy tsinghal anemajerova fcherat kkamate pmao tslewis anfrenkel fcornejofern kkannapur pmarla tsmiley angderosa fcoskun kkasarapu pmatera tteng aniksingh feliang kkasavajhala pmcdowall tthakir anisrinivasa fenzhang kkaushik pmdunge tthulasidas anjmoore fewang kkayang pmeade ttnnguyen ankmaheshwar feyeh kkirane pmeda ttom ankrishnan fgao kkostyszyn pmmehta tweinacht anltran fhchaudhry kkui pmscully tweiwei annicoll fiburke kkurti pmuzac twymore anpnguyen fiowong kkyeong pnalluri txiang anpurwar fjalia klanzetta pnookala tye ansabharwal fjangchup klhudson podonnell tyeh ansgandhi fkarankumar kljjohnson ppolak tyokoyama anshen fkhondker kllivichuzca ppriyadarshi tzwei anslade fladeind kmadanahitib praagarwal uarora anthochen fluo kmardysilofa pragupta uarora.OLD antmunoz fmaisha kmasarik praroy ugarg antzhu fmlopez kmbala pratagarwal ukadakia anurizada fmnoor kmchang pratkumar umoll anvinod fnieto kmchau priyjain umukherjee anzaman forabona kmcneil prkkumar upoddar anzhu fpocaamoros kmfallon prmukhopadhy urasheed anzzhou frdominguezg kmhayes prouth urehman aokisamen frhu kmsimon prreddy urosani apaddayurush frobayobohor kmueller psahu ushafiq apaddayurush.OLD fsotiropoulo kmungsoo psamang ushassan apagarwal fuliang kmurgas psangtani usunar apalit fwelcome kpallmann psekar utegshbayar apalo fzali kpinzon pshanbhogue utumuluri apalve gacolella kpipitone pskota uuckun apamfilie gahuja kprose psmeyer uyevarouskay aperezantona gakapoor kralbano psokol vachandramou apettenati gakhan kramcharan psonawane vadabala aphope galing krayfield psoundarapan vanlin apilco 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zilwu danizheng jinkokim molssi039 siyimaya zirliu dantorres jinwang2 morahimi siyzou zishao dantyu jinwei moriasaranib sizahid ziweiwang danwei jinyhu mozhao sizzheng ziwyu daoconnell jinyinwang mperess sjaffary zixli dappark jinyli mpersch sjamshad ziyli darkow jinyuyang mpetrusky sjeevan ziyozhang darlin jinyxu mpkatz sjens ziyye darvind jinzwang mpsantomauro sjiecheng zkrayem darzeng jiqian mquispecarba sjnelson zlyu dathanasakos jiychong mradfar sjyang zmou daultmccoy jiyim mrahimibolda skade zniu davidlin jiyjung mrakhar skagana zoanderson davizhao jiyounpark mrashid skalam zoxie davliang jiyuliu mrathore skalva zqiao davsilverman jiyuyang mrayeesuddin skann zsongzhu dawan jjcarter mrehan skapse zuzheng dawei jjguo mreuter skapur zwray dawendt jjjones mrichter skarnik zye dawhu jjnielsen mrius skatariya zzaidi daxxie jkable mrkumar skavuri zzhuang dayeung jkiryluk mrosati sketchum zzoya dayyan jkodner mrsun skobayashi dayyoon jkohara msardis skogilathota dbasu jkonopka msavenkov skomatireddy dbluestein jkottmann msayana skoppuravuri (base) [ehspector@milan1 home]$ cd .. (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/ (base) [ehspector@milan1 AMS536]$ ls 1EVE_Lig_nH.mol2 1eve_Rec_nH.mol2 2018 2021 2024 junk.txt 1EVE_Lig_wH.mol2 1eve_Rec_wH.mol2 2019 2022 2025 zzz.anchors 1EVE_Rec_nHDMS.dms 2017 2020 2023 get_anchors.py zzz.programs (base) [ehspector@milan1 AMS536]$ cd 2025 (base) [ehspector@milan1 2025]$ ls 1EVE_DOCK_VS INSPH rotations wed_humpday.txt additional_files robbashrc_file test4.tar (base) [ehspector@milan1 2025]$ vi test4.tar (base) [ehspector@milan1 2025]$ pwd /gpfs/projects/AMS536/2025 (base) [ehspector@milan1 2025]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/test4.tar test4.tar (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN test4.tar (base) [ehspector@milan1 Tutorials]$ mv test4.tar 2w26/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Notes.txt 002_surface_spheres 005_rigid 008_rescore test4.tar 003_gridbox 006_flex_docking commands.txt (base) [ehspector@milan1 2w26]$ tar -xf test4.tar (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_cartesian_min commands.txt 002_surface_spheres 005_rigid 008_rescore Notes.txt 003_gridbox 006_flex_docking 2W26 test4.tar (base) [ehspector@milan1 2w26]$ cd 2W26/ (base) [ehspector@milan1 2W26]$ ls 001_structure 002_spheres 003_grid 004_dock (base) [ehspector@milan1 2W26]$ cd 004_dock/ (base) [ehspector@milan1 004_dock]$ ls 01fps_footprint_scored.txt 01fps_scored.mol2 02rgd.in 03fad.out 01fps_footprint_scored.txt.pdf 01fps.sh 02rgd.log 03fad_scored.mol2 01fps_hbond_scored.txt 01min.in 02rgd.out 03fad.sh 01fps.in 01min.log 02rgd_scored.mol2 04flx.in 01fps.log1 01min.out 02rgd.sh 04flx.sh 01fps.log2 01min_scored.mol2 03fad.in old_01min.in 01fps.out 01min.sh 03fad.log (base) [ehspector@milan1 004_dock]$ vi 02rgd.in (base) [ehspector@milan1 004_dock]$ cd ../../ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_cartesian_min commands.txt 002_surface_spheres 005_rigid 008_rescore Notes.txt 003_gridbox 006_flex_docking 2W26 test4.tar (base) [ehspector@milan1 2w26]$ mv 005_rigid/ 005_dock/ (base) [ehspector@milan1 2w26]$ mv 006_flex_docking/ 006_virtual_screening (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_cartesian_min commands.txt 002_surface_spheres 005_dock 008_rescore Notes.txt 003_gridbox 006_virtual_screening 2W26 test4.tar (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_2w26 (base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/02rgd.in 005_dock/ (base) [ehspector@milan1 2w26]$ cd 005_dock/ (base) [ehspector@milan1 005_dock]$ ls 02rgd.in rigid.in rigid.out_conformers.mol2 rigid.sh rigid_2.sh rigid.out rigid.out_scored.mol2 (base) [ehspector@milan1 005_dock]$ rm rigid.in (base) [ehspector@milan1 005_dock]$ mv 02rgd.in rigid.in (base) [ehspector@milan1 005_dock]$ ls rigid_2.sh rigid.in rigid.out rigid.out_conformers.mol2 rigid.out_scored.mol2 rigid.sh (base) [ehspector@milan1 005_dock]$ rm rigid.out_conformers.mol2 (base) [ehspector@milan1 005_dock]$ rm rigid.out_scored.mol2 (base) [ehspector@milan1 005_dock]$ vi rigid.in (base) [ehspector@milan1 005_dock]$ ls rigid_2.sh rigid.in rigid.out rigid.sh (base) [ehspector@milan1 005_dock]$ cd .. (base) [ehspector@milan1 2w26]$ cd 001_structure/ (base) [ehspector@milan1 001_structure]$ la -bash: la: command not found (base) [ehspector@milan1 001_structure]$ ls 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd ../005_dock/ (base) [ehspector@milan1 005_dock]$ ls rigid_2.sh rigid.in rigid.out rigid.sh (base) [ehspector@milan1 005_dock]$ vi rigid.in (base) [ehspector@milan1 005_dock]$ mkdir rigid_docking (base) [ehspector@milan1 005_dock]$ mv rigid.in rigid_docking/ (base) [ehspector@milan1 005_dock]$ mv rigid.sh rigid_docking/ (base) [ehspector@milan1 005_dock]$ mv rigid_2.sh rigid_docking/ (base) [ehspector@milan1 005_dock]$ rm rigid.out (base) [ehspector@milan1 005_dock]$ ls rigid_docking (base) [ehspector@milan1 005_dock]$ mkdir flex_docking (base) [ehspector@milan1 005_dock]$ mkdir_fixed_anchor_docking -bash: mkdir_fixed_anchor_docking: command not found (base) [ehspector@milan1 005_dock]$ mkdir fixed_anchor_docking (base) [ehspector@milan1 005_dock]$ ls fixed_anchor_docking flex_docking rigid_docking (base) [ehspector@milan1 005_dock]$ cd rigid_docking/ (base) [ehspector@milan1 rigid_docking]$ ls rigid_2.sh rigid.in rigid.sh (base) [ehspector@milan1 rigid_docking]$ vi rigid.in (base) [ehspector@milan1 rigid_docking]$ vi rigid_2.sh (base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh (base) [ehspector@milan1 rigid_docking]$ ls rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh (base) [ehspector@milan1 rigid_docking]$ vi rigid.out (base) [ehspector@milan1 rigid_docking]$ vi rigid.in (base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh (base) [ehspector@milan1 rigid_docking]$ ls rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh (base) [ehspector@milan1 rigid_docking]$ vi rigid.out (base) [ehspector@milan1 rigid_docking]$ vi rigid.in (base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh (base) [ehspector@milan1 rigid_docking]$ ls rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh (base) [ehspector@milan1 rigid_docking]$ grep -c "Name" rigid_scored.mol2 7 (base) [ehspector@milan1 rigid_docking]$ cd .. (base) [ehspector@milan1 005_dock]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Notes.txt 002_surface_spheres 005_dock 008_rescore Robs_2w26 003_gridbox 006_virtual_screening commands.txt test4.tar (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/03fad.in 005_dock/fixed_anchor_docking/ (base) [ehspector@milan1 2w26]$ cd 005_dock/fixed_anchor_docking/ (base) [ehspector@milan1 fixed_anchor_docking]$ ls 03fad.in (base) [ehspector@milan1 fixed_anchor_docking]$ mv 03fad.in fad.in (base) [ehspector@milan1 fixed_anchor_docking]$ cd .. (base) [ehspector@milan1 005_dock]$ cp rigid_docking/rigid_2.sh fixed_anchor_docking/fad.sh (base) [ehspector@milan1 005_dock]$ cd fixed_anchor_docking/ (base) [ehspector@milan1 fixed_anchor_docking]$ ls fad.in fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.in (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ bash fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ ls fad.in fad.out fad_scored.mol2 fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.out (base) [ehspector@milan1 fixed_anchor_docking]$ cd .. (base) [ehspector@milan1 005_dock]$ cp fixed_anchor_docking/fad.sh flex_docking/flex.sh (base) [ehspector@milan1 005_dock]$ cd .. (base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/04flx.in 005_dock/flex_docking/flex.in (base) [ehspector@milan1 2w26]$ cd 005_dock/flex_docking/ (base) [ehspector@milan1 flex_docking]$ ls flex.in flex.sh (base) [ehspector@milan1 flex_docking]$ vi flex.in (base) [ehspector@milan1 flex_docking]$ vi flex.sh (base) [ehspector@milan1 flex_docking]$ bash flex.sh (base) [ehspector@milan1 flex_docking]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan1 flex_docking]$ grep -c "Name" flex_scored.mol2 20 (base) [ehspector@milan1 flex_docking]$ cd .. (base) [ehspector@milan1 005_dock]$ cd flex_docking/ (base) [ehspector@milan1 flex_docking]$ pwd /gpfs/home/ehspector/AMS_536/Tutorials/2w26/005_dock/flex_docking (base) [ehspector@milan1 flex_docking]$ cd ../fixed_anchor_docking/ (base) [ehspector@milan1 fixed_anchor_docking]$ ls fad.in fad.out fad_scored.mol2 fad.sh (base) [ehspector@milan1 fixed_anchor_docking]$ cd ../rigid_docking/ (base) [ehspector@milan1 rigid_docking]$ ls rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh (base) [ehspector@milan1 rigid_docking]$ cd ../../ (base) [ehspector@milan1 2w26]$ cd ../ (base) [ehspector@milan1 Tutorials]$ cd 5EEN/ (base) [ehspector@milan1 5EEN]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan1 5EEN]$ mv 005_virtual_screen/ 005_dock (base) [ehspector@milan1 5EEN]$ cd 005_dock/ (base) [ehspector@milan1 005_dock]$ ls (base) [ehspector@milan1 005_dock]$ mkdir rigid fixed_anchor flex (base) [ehspector@milan1 005_dock]$ ls fixed_anchor flex rigid (base) [ehspector@milan1 005_dock]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid_2.sh 5EEN/005_dock/rigid/ (base) [ehspector@milan1 Tutorials]$ cd 5EEN/005_dock/rigid/ (base) [ehspector@milan1 rigid]$ ls rigid_2.sh (base) [ehspector@milan1 rigid]$ vi rigid_2.sh (base) [ehspector@milan1 rigid]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 5EEN (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 5EEN]$ cd 005_dock/ (base) [ehspector@milan2 005_dock]$ ls fixed_anchor flex rigid (base) [ehspector@milan2 005_dock]$ cd rigid/ (base) [ehspector@milan2 rigid]$ ls rigid_2.sh (base) [ehspector@milan2 rigid]$ touch rigid.in (base) [ehspector@milan2 rigid]$ vi rigid_2.sh (base) [ehspector@milan2 rigid]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i rigid.in

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Molecule Library Input Parameters

                                            ligand_atom_file [database.mol2] ():5EEN.lig.min_scored.mol2
                                           limit_max_ligands [no] (yes no):
                                               skip_molecule [no] (yes no):
                                          read_mol_solvation [no] (yes no):
                                              calculate_rmsd [no] (yes no):yes
                                      use_rmsd_reference_mol [no] (yes no):yes
                                     rmsd_reference_filename [ligand_rmsd.mol2] ():5EEN.lig.min_scored.mol2

Database Filter Parameters

                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):
                                          automated_matching [yes] (yes no):
                                          receptor_site_file [receptor.sph] ():../../002_surface_spheres/selected_spheres.sph
                                            max_orientations [1000] ():
                                             critical_points [no] (yes no):
                                           chemical_matching [no] (yes no):
                                          use_ligand_spheres [no] (yes no):

Bump Filter Parameters

                                                 bump_filter [no] (yes no):

Master Score Parameters

                                             score_molecules [yes] (yes no):

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):
                                    grid_score_rep_rad_scale [1] ():
                                        grid_score_vdw_scale [1] ():
                                         grid_score_es_scale [1] ():
                                         grid_lig_efficiency [no] (yes no):
                                      grid_score_grid_prefix [grid] ():../../003_gridbox/grid

GIST Score Parameters

MultiGrid Score Parameters

Dock3.5 Score Parameters

Continuous Energy Score Parameters

Footprint Similarity Score Parameters

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

                                             minimize_ligand [yes] (yes no):yes
                                      simplex_max_iterations [1000] ():
                              simplex_tors_premin_iterations [0] ():
                                          simplex_max_cycles [1] ():
                                      simplex_score_converge [0.1] ():
                                      simplex_cycle_converge [1.0] ():
                                          simplex_trans_step [1.0] ():
                                            simplex_rot_step [0.1] ():
                                           simplex_tors_step [10.0] ():
                                           simplex_final_min [no] (yes no):
                                         simplex_random_seed [0] ():
                                       simplex_restraint_min [no] (yes no):

Atom Typing Parameters

                                                  atom_model [all] (all | united):
                                               vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
                                              flex_defn_file [flex.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn 
                                             flex_drive_file [flex_drive.tbl] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

                                       ligand_outfile_prefix [output] ():rigid
                                         write_mol_solvation [no] (yes no):
                                          write_orientations [no] (yes no):
                                       num_scored_conformers [1] ():
                                             score_threshold [100.0] ():
                                                rank_ligands [no] (yes no):

Initializing Library File Routines...

Could not open 5EEN.lig.min_scored.mol2 for reading. Program will terminate.

(base) [ehspector@milan2 rigid]$ cd ../../004_energymin/ (base) [ehspector@milan2 004_energymin]$ ls 5een.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan2 004_energymin]$ cd ../005_dock/rigid/ (base) [ehspector@milan2 rigid]$ ls rigid_2.sh rigid.in (base) [ehspector@milan2 rigid]$ vi rigid.in (base) [ehspector@milan2 rigid]$ vi rigid.in (base) [ehspector@milan2 rigid]$ bash rigid_2.sh (base) [ehspector@milan2 rigid]$ ls rigid_2.sh rigid.in rigid.out (base) [ehspector@milan2 rigid]$ vi rigid.out (base) [ehspector@milan2 rigid]$ vi rigid.in (base) [ehspector@milan2 rigid]$ bash rigid_2.sh (base) [ehspector@milan2 rigid]$ ls rigid_2.sh rigid.in rigid.out rigid_scored.mol2 (base) [ehspector@milan2 rigid]$ vi rigid.out (base) [ehspector@milan2 rigid]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/ (base) [ehspector@milan2 rigid]$ rm rigid.in (base) [ehspector@milan2 rigid]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid.in 5EEN/005_dock/rigid/rigid.in (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/ (base) [ehspector@milan2 rigid]$ ls rigid_2.sh rigid.in rigid.out rigid_scored.mol2 (base) [ehspector@milan2 rigid]$ vi rigid.in (base) [ehspector@milan2 rigid]$ bash rigid_2.sh (base) [ehspector@milan2 rigid]$ ls rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 (base) [ehspector@milan2 rigid]$ grep -c "Name" rigid_scored.mol2 19 (base) [ehspector@milan2 rigid]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.in 5EEN/005_dock/fixed_anchor/fad.in (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.sh 5EEN/005_dock/fixed_anchor/fad.sh (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/fixed_anchor/ (base) [ehspector@milan2 fixed_anchor]$ ls fad.in fad.sh (base) [ehspector@milan2 fixed_anchor]$ vi fad.in (base) [ehspector@milan2 fixed_anchor]$ vi fad.sh (base) [ehspector@milan2 fixed_anchor]$ bash fad.sh (base) [ehspector@milan2 fixed_anchor]$ ls fad.in fad.out fad_scored.mol2 fad.sh (base) [ehspector@milan2 fixed_anchor]$ grep -c "Name" fad_scored.mol2 7 (base) [ehspector@milan2 fixed_anchor]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.in 5EEN/005_dock/flex/flex.in (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.sh 5EEN/005_dock/flex/flex.sh (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/ (base) [ehspector@milan2 flex]$ ls flex.in flex.sh (base) [ehspector@milan2 flex]$ vi flex.in (base) [ehspector@milan2 flex]$ bash flex.sh exit (base) [ehspector@milan2 flex]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/ (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2 3 (base) [ehspector@milan2 flex]$ vi flex.out (base) [ehspector@milan2 flex]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/ (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ rm flex.out (base) [ehspector@milan2 flex]$ bash flex.sh (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ vi flex. (base) [ehspector@milan2 flex]$ vi flex.out (base) [ehspector@milan2 flex]$ cd .. (base) [ehspector@milan2 005_dock]$ ls fixed_anchor flex rigid (base) [ehspector@milan2 005_dock]$ cd flex/ (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 1O86]$ mv 005_virtual_screen/ 005_dock (base) [ehspector@milan2 1O86]$ cd 005_dock/ (base) [ehspector@milan2 005_dock]$ mkdir rigid fixed_anchor flex (base) [ehspector@milan2 005_dock]$ cd ../../ (base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.in 1O86/005_dock/rigid/rigin.in (base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.sh 1O86/005_dock/rigid/rigin.sh cp: cannot stat '5EEN/005_dock/rigid/rigid.sh': No such file or directory (base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid_2.sh 1O86/005_dock/rigid/rigin.sh (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 1O86/005_dock/rigid/ (base) [ehspector@milan2 rigid]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP AMS_548 % cd ../AMS_691 (base) supremestudier@Evans-MBP AMS_691 % ls AMS691_01.pdf Lectures Projects Text_book (base) supremestudier@Evans-MBP AMS_691 % mkdir PyTorch (base) supremestudier@Evans-MBP AMS_691 % cd ../AMS_536 (base) supremestudier@Evans-MBP AMS_536 % ls Tutorial project.example.dGhyd.pdf project.example.MMPS.pdf zzz_2025_01_29a_seawulf_notes.docx (base) supremestudier@Evans-MBP AMS_536 % cd Tutorial (base) supremestudier@Evans-MBP Tutorial % ls 1O86 2w26 5EEN folders.txt (base) supremestudier@Evans-MBP Tutorial % cd 5EEN (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ cd 1O86/005_dock/rigid/ -bash: cd: 1O86/005_dock/rigid/: No such file or directory (base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd 1O86/005_dock/rigid/ -bash: cd: 1O86/005_dock/rigid/: No such file or directory (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/rigid/ (base) [ehspector@milan1 rigid]$ ls rigin.in rigin.sh (base) [ehspector@milan1 rigid]$ mv rigin.in rigid.in (base) [ehspector@milan1 rigid]$ mv rigin.sh rigid.sh (base) [ehspector@milan1 rigid]$ vi rigid.in (base) [ehspector@milan1 rigid]$ cd ../../004_energymin/ (base) [ehspector@milan1 004_energymin]$ ls 1O86.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan1 004_energymin]$ cd ../005_dock/rigid/ (base) [ehspector@milan1 rigid]$ ls rigid.in rigid.sh (base) [ehspector@milan1 rigid]$ vi rigid.sh (base) [ehspector@milan1 rigid]$ bash rigid.sh (base) [ehspector@milan1 rigid]$ ls rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh (base) [ehspector@milan1 rigid]$ vi rigid.out (base) [ehspector@milan1 rigid]$ grep -c "Name" rigid_scored.mol2 7 (base) [ehspector@milan1 rigid]$ cd .. (base) [ehspector@milan1 005_dock]$ cd ../../ (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.in 1O86/005_dock/fixed_anchor/fad.in (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.sh 1O86/005_dock/fixed_anchor/fad.sh (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.in 1O86/005_dock/flex/flex.in (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.sh 1O86/005_dock/flex/flex.sh (base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/fixed_anchor/ (base) [ehspector@milan1 fixed_anchor]$ ls fad.in fad.sh (base) [ehspector@milan1 fixed_anchor]$ vi fad.in (base) [ehspector@milan1 fixed_anchor]$ bash fad.sh (base) [ehspector@milan1 fixed_anchor]$ cd .. (base) [ehspector@milan1 005_dock]$ cd fixed_anchor/ (base) [ehspector@milan1 fixed_anchor]$ ls fad.in fad.out fad_scored.mol2 fad.sh (base) [ehspector@milan1 fixed_anchor]$ grep -c "Name" fad_scored.mol2 3 (base) [ehspector@milan1 fixed_anchor]$ cd .. (base) [ehspector@milan1 005_dock]$ cd flex/ (base) [ehspector@milan1 flex]$ ls flex.in flex.sh (base) [ehspector@milan1 flex]$ vi flex.in (base) [ehspector@milan1 flex]$ bash flex.sh ^C^X (base) [ehspector@milan1 flex]$ vi flex.in (base) [ehspector@milan1 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan1 flex]$ rm flex.out (base) [ehspector@milan1 flex]$ bash flex.sh (base) [ehspector@milan1 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan1 flex]$ vi flex.out (base) [ehspector@milan1 flex]$ grep -c "Name" flex_scored.mol2 32 (base) [ehspector@milan1 flex]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ cd 2w26/005_dock/flex_docking/ (base) [ehspector@milan1 flex_docking]$ vi flex.in (base) [ehspector@milan1 flex_docking]$ cd .. (base) [ehspector@milan1 005_dock]$ cd ../../5EEN/005_dock/flex/ (base) [ehspector@milan1 flex]$ vi flex.in (base) [ehspector@milan1 flex]$ exit (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in...

- - - IMPORTANT MESSAGE BELOW****

In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.

(base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/ (base) [ehspector@login2 install]$ ls bluegenel gnu.acml homebrew intel.mkl sgi bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel config.h gnu.parallel ibmaix Makefile test configure gnu.parallel.rdkit intel oneapi docker gnu.rdkit intel.intelmpi.parallel pgi gnu gnu.valgrind intel.ip.mkl rules.h (base) [ehspector@login2 install]$ ./configure gnu The requested configuration file was found.

Warning: the configuration file already exists with the creation stamp:

Created at Mon Jan 20 04:34:02 PM EST 2025 via ./configure gnu.rdkit

It will be overwritten !

Don't forget to make clean before rebuilding. To reconfigure and rebuild everything start with make -i distclean: Reconfiguring after make -i distclean will avoid this warning.

The DOCK configuration file has been created. (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Wed Feb 12 10:29:40 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp g++ -c -O2 -std=c++11 -o filter.o filter.cpp g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp g++ -c -O2 -std=c++11 -o grid.o grid.cpp g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp g++ -c -O2 -std=c++11 -o orient.o orient.cpp g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp g++ -c -O2 -std=c++11 -o score.o score.cpp g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -o trace.o trace.cpp g++ -c -O2 -std=c++11 -o utils.o utils.cpp g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp cd nab && make all make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -lm -lpthread mv dock6 ../../bin make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Wed Feb 12 10:31:34 EST 2025.

(base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd .. (base) [ehspector@login2 src]$ cd ../install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Wed Feb 12 10:33:23 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:550:9: error: ‘num_zeros’ was not declared in this scope

 550 |     if (num_zeros == mol.num_atoms){
     |         ^12:36, 21 February 2025 (EST)Stonybrook (talk)

make[1]: *** [dockmol.o] Error 1 make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [dock] Error 2 (base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd ../ (base) [ehspector@login2 src]$ cd ../install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Wed Feb 12 10:36:16 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp g++ -c -O2 -std=c++11 -o filter.o filter.cpp g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp g++ -c -O2 -std=c++11 -o grid.o grid.cpp g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp g++ -c -O2 -std=c++11 -o orient.o orient.cpp g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp g++ -c -O2 -std=c++11 -o score.o score.cpp g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -o trace.o trace.cpp g++ -c -O2 -std=c++11 -o utils.o utils.cpp g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp cd nab && make all make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -lm -lpthread mv dock6 ../../bin make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Wed Feb 12 10:38:00 EST 2025.

(base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd ,, -bash: cd: ,,: No such file or directory (base) [ehspector@login2 alpha_branch]$ home (base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_4.in gas.in no_gas.out_scored.mol2 1AAQ_yesG.mol2 gas_4.out gas.out test.mol2 gas_2.in gas_4.out_scored.mol2 gas.out_scored.mol2 test_nocharge.mol2 gas_2.out gas_5.in no_charge gas_3.in gas_5.out no_gas.in gas_3.out gas_5.out_scored.mol2 no_gas.out (base) [ehspector@login2 gas_teiger]$ vi gas_4.out (base) [ehspector@login2 gas_teiger]$ rm gas_4.out (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas.out (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.out_scored.mol2 no_gas.in 1AAQ_yesG.mol2 gas_4.in gas.in no_gas.out gas_2.in gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 gas_2.out gas_5.in gas.out_scored.mol2 test.mol2 gas_3.in gas_5.out no_charge test_nocharge.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_4.out (base) [ehspector@login2 gas_teiger]$ vi gas_4.in (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_4.in (base) [ehspector@login2 gas_teiger]$ vi gas_5.in (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2 (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2 (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_5.in -o gas_5.out (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.out_scored.mol2 no_gas.in 1AAQ_yesG.mol2 gas_4.in gas.in no_gas.out gas_2.in gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 gas_2.out gas_5.in gas.out_scored.mol2 test.mol2 gas_3.in gas_5.out no_charge test_nocharge.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_5.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_5.in (base) [ehspector@login2 gas_teiger]$ vi gas_4.in (base) [ehspector@login2 gas_teiger]$ vi gas_4.in (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_4.in gas.in no_gas.out_scored.mol2 1AAQ_yesG.mol2 gas_4.out gas.out test.mol2 gas_2.in gas_4.out_scored.mol2 gas.out_scored.mol2 test_nocharge.mol2 gas_2.out gas_5.in no_charge gas_3.in gas_5.out no_gas.in gas_3.out gas_5.out_scored.mol2 no_gas.out (base) [ehspector@login2 gas_teiger]$ vi gas_4.out (base) [ehspector@login2 gas_teiger]$ cd .. (base) [ehspector@login2 4s0v]$ cd .. (base) [ehspector@login2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@login2 dock]$ vi filter.cpp (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd .. (base) [ehspector@login2 src]$ cd ../install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Wed Feb 12 10:49:54 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:542:5: error: ‘If’ was not declared in this scope

 542 |     If all partial charges are zero, it is a bad molecule
     |     ^~

dockmol.cpp:546:13: error: ‘num_zeros’ was not declared in this scope

 546 |             num_zeros += 1;
     |             ^12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp:549:6: error: ‘Is’ was not declared in this scope

 549 |      Is it a bad molecule?
     |      ^~

dockmol.cpp:552:7: error: ‘else’ without a previous ‘if’

 552 |     } else {
     |       ^Stonybrook (talk)

make[1]: *** [dockmol.o] Error 1 make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [dock] Error 2 (base) [ehspector@login2 install]$ cd ../src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd .. (base) [ehspector@login2 src]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd src/dock (base) [ehspector@login2 dock]$ cd ../../ (base) [ehspector@login2 alpha_branch]$ cd install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Wed Feb 12 10:52:33 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp g++ -c -O2 -std=c++11 -o filter.o filter.cpp g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp g++ -c -O2 -std=c++11 -o grid.o grid.cpp g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp g++ -c -O2 -std=c++11 -o orient.o orient.cpp g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp g++ -c -O2 -std=c++11 -o score.o score.cpp g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -o trace.o trace.cpp g++ -c -O2 -std=c++11 -o utils.o utils.cpp g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp cd nab && make all make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -lm -lpthread mv dock6 ../../bin make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Wed Feb 12 10:54:21 EST 2025.

(base) [ehspector@login2 install]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in...

- - - IMPORTANT MESSAGE BELOW****

In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.

(base) [ehspector@login1 ~]$ home (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/ (base) [ehspector@login1 src]$ ls accessories antechamber dock docktools gbsa_grids grid Makefile mopac6 rdkit resp tleap (base) [ehspector@login1 src]$ cd dock (base) [ehspector@login1 dock]$ ls amber_typer.cpp defreal.h iso_align.o README score.o amber_typer.h dock.cpp library_file.cpp sasa.cpp score_ph4.cpp amber_typer.o dockmol.cpp library_file.h sasa.h score_ph4.h base_grid.cpp dockmol.h library_file.o sasa.o score_ph4.o base_grid.h dockmol.o limit_max_change.cpp score_amber.cpp score_sasa.cpp base_grid.o dock.o limit_max_change.h score_amber.h score_sasa.h base_mpi.cpp filter.cpp limit_max_change.o score_amber.o score_sasa.o base_mpi.h filter.h lol score_chemgrid.cpp score_solvent.cpp base_mpi.o filter.o Makefile score_chemgrid.h score_solvent.h base_score.cpp fingerprint.cpp master_conf.cpp score_chemgrid.o score_solvent.o base_score.h fingerprint.h master_conf.h score.cpp score_volume.cpp base_score.o fingerprint.o master_conf.o score_descriptor.cpp score_volume.h conf_gen_ag.cpp fraggraph.cpp master_score.cpp score_descriptor.h score_volume.o conf_gen_ag.h fraggraph.h master_score.h score_descriptor.o simplex.cpp conf_gen_ag.o fraggraph.o master_score.o score_footprint.cpp simplex.h conf_gen_cg.cpp fragment.cpp mem_info.cpp score_footprint.h simplex.o conf_gen_cg.h fragment.h mem_info.h score_footprint.o sphere.cpp conf_gen_cg.o fragment.o mem_info.o score_gist.cpp sphere.h conf_gen_dn.cpp gasteiger.cpp nab score_gist.h sphere.o conf_gen_dn_ga.cpp gasteiger.h nabcode.h score_gist.o tnt conf_gen_dn_ga.h gasteiger.o nab.h score.h trace.cpp conf_gen_dn_ga.o grid.cpp orient.cpp score_hbond.cpp trace.h conf_gen_dn.h grid.h orient.h score_hbond.h trace.inl conf_gen_dn.o grid.o orient.o score_hbond.o trace.o conf_gen_ga.cpp gzstream rddrive.cpp score_internal.cpp utils.cpp conf_gen_ga.h hungarian.cpp rddrive.h score_internal.h utils.h conf_gen_ga.o hungarian.h rddrive.o score_internal.o utils.o conf_gen_hdb.cpp hungarian.o rdtyper.cpp score_multigrid.cpp version.h conf_gen_hdb.h iso_align.cpp rdtyper.h score_multigrid.h xlogp.cpp conf_gen_hdb.o iso_align.h rdtyper.o score_multigrid.o xlogp.h (base) [ehspector@login1 dock]$ vi dockmol.cpp (base) [ehspector@login1 dock]$ cd ../../install/ (base) [ehspector@login1 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login1 install]$ make dock Starting installation of DOCK v6.12 program dock at Wed Feb 12 13:24:37 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp g++ -c -O2 -std=c++11 -o filter.o filter.cpp g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp g++ -c -O2 -std=c++11 -o grid.o grid.cpp g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp g++ -c -O2 -std=c++11 -o orient.o orient.cpp g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp g++ -c -O2 -std=c++11 -o score.o score.cpp g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -o trace.o trace.cpp g++ -c -O2 -std=c++11 -o utils.o utils.cpp g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp cd nab && make all make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -lm -lpthread mv dock6 ../../bin make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Wed Feb 12 13:27:09 EST 2025.

(base) [ehspector@login1 install]$ cd .. (base) [ehspector@login1 alpha_branch]$ cd ../../4s0v/gas_teiger/ (base) [ehspector@login1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.out no_charge test_nocharge.mol2 1AAQ_yesG.mol2 gas_4.in gas_5.out_scored.mol2 no_gas.in gas_2.in gas_4.out gas.in no_gas.out gas_2.out gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 gas_3.in gas_5.in gas.out_scored.mol2 test.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas_4.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@login1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.out no_charge test_nocharge.mol2 1AAQ_yesG.mol2 gas_4.in gas_5.out_scored.mol2 no_gas.in gas_2.in gas_4.out gas.in no_gas.out gas_2.out gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 gas_3.in gas_5.in gas.out_scored.mol2 test.mol2 (base) [ehspector@login1 gas_teiger]$ vi 1AAQ_noG.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas_4.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas_3.in (base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas_3.in (base) [ehspector@login1 gas_teiger]$ vi gas_3.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out (base) [ehspector@login1 gas_teiger]$ vi gas_3.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2 (base) [ehspector@login1 gas_teiger]$ vi test.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas_2.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@login1 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.in gas.out_scored.mol2 test.mol2 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out no_charge test_nocharge.mol2 gas_2.in gas_4.in gas_5.out_scored.mol2 no_gas.in gas_2.out gas_4.out gas.in no_gas.out gas_3.in gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ vi gas_2.in (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out (base) [ehspector@login1 gas_teiger]$ vi gas_2.out_scored.mol2 (base) [ehspector@login1 gas_teiger]$ cd .. (base) [ehspector@login1 4s0v]$ cd ../../ (base) [ehspector@login1 rizzo]$ home (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/ accessories/ dock/ gbsa_grids/ mopac6/ resp/ antechamber/ docktools/ grid/ rdkit/ tleap/ (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/ accessories/ dock/ gbsa_grids/ mopac6/ resp/ antechamber/ docktools/ grid/ rdkit/ tleap/ (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/ accessories/ dock/ gbsa_grids/ mopac6/ resp/ antechamber/ docktools/ grid/ rdkit/ tleap/ (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@login1 dock]$ vi dockmol.cpp \(base) [ehspector@login1 dock]$ vi filter.cpp (base) [ehspector@login1 dock]$ vi library_file.cpp (base) [ehspector@login1 dock]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP 5EEN % ls 5een.lig.min_scored.mol2 5een_noH_nocH.mol2 5een.pdb 5een_protein_only.pdb 5een.sph 5een_surface.dms 5een_H_cH.mol2 fad_scored.mol2 5een_ligand_H_cH.mol2 flex_scored.mol2 5een_ligand_noH_nocH.mol2 rigid_scored.mol2 5een_ligand_only.pdb selected_spheres.sph (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 1O86]$ cd 005_dock/ (base) [ehspector@milan2 005_dock]$ cd rigid/ (base) [ehspector@milan2 rigid]$ ls rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh (base) [ehspector@milan2 rigid]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd .. (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/ (base) [ehspector@milan2 flex]$ vi flex.out (base) [ehspector@milan2 flex]$ vi flex.in (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ rm flex.out (base) [ehspector@milan2 flex]$ bash flex.sh (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ vi flex.out (base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2 46 (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ vi flex.sh (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ ls flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh (base) [ehspector@milan2 flex]$ which dock6 /gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6 (base) [ehspector@milan2 flex]$ vi ~/.bashrc (base) [ehspector@milan2 flex]$ cd .. (base) [ehspector@milan2 005_dock]$ cd .. (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Notes.txt 002_surface_spheres 005_dock 008_rescore Robs_2w26 003_gridbox 006_virtual_screening commands.txt test4.tar (base) [ehspector@milan2 2w26]$ cd 004_energymin/ (base) [ehspector@milan2 004_energymin]$ ls 2w26.lig.min_scored.mol2 min.in min.out min.sh (base) [ehspector@milan2 004_energymin]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Notes.txt 002_surface_spheres 005_dock 008_rescore Robs_2w26 003_gridbox 006_virtual_screening commands.txt test4.tar (base) [ehspector@milan2 2w26]$ mv 006_virtual_screening/ 006_footprint (base) [ehspector@milan2 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Notes.txt 002_surface_spheres 005_dock 008_rescore Robs_2w26 003_gridbox 006_footprint commands.txt test4.tar (base) [ehspector@milan2 2w26]$ cd 006_footprint/ (base) [ehspector@milan2 006_footprint]$ touch footprint.in (base) [ehspector@milan2 006_footprint]$ ls footprint.in (base) [ehspector@milan2 006_footprint]$ cd .. (base) [ehspector@milan2 2w26]$ cp 003_gridbox/grid.sh 006_footprint/foot.sh (base) [ehspector@milan2 2w26]$ cd 006_footprint/ (base) [ehspector@milan2 006_footprint]$ vi foot.sh (base) [ehspector@milan2 006_footprint]$ vi foot.sh (base) [ehspector@milan2 006_footprint]$ class (base) [ehspector@milan2 AMS_536]$ ls class_project Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd .. (base) [ehspector@milan2 AMS_536]$ cd class_project/ (base) [ehspector@milan2 class_project]$ ls (base) [ehspector@milan2 class_project]$ ls (base) [ehspector@milan2 class_project]$ cd .. (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Notes.txt 002_surface_spheres 005_dock 008_rescore Robs_2w26 003_gridbox 006_footprint commands.txt test4.tar (base) [ehspector@milan2 2w26]$ mv Notes.txt ../../ (base) [ehspector@milan2 2w26]$ mv commands.txt ../../ (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min Robs_2w26 002_surface_spheres 004_energymin 006_footprint 008_rescore test4.tar (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd .. (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ vi Notes.txt (base) [ehspector@milan2 AMS_536]$ vi commands.txt (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min Robs_2w26 002_surface_spheres 004_energymin 006_footprint 008_rescore test4.tar (base) [ehspector@milan2 2w26]$ mkdir 007_virtual_screen (base) [ehspector@milan2 2w26]$ ls 001_structure 004_energymin 007_cartesian_min Robs_2w26 002_surface_spheres 005_dock 007_virtual_screen test4.tar 003_gridbox 006_footprint 008_rescore (base) [ehspector@milan2 2w26]$ mv 007_cartesian_min/ 008_cartesian_min (base) [ehspector@milan2 2w26]$ mv 008_rescore/ 009_rescore (base) [ehspector@milan2 2w26]$ cd ../5EEN/ (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 5EEN]$ mv 006_virtual_screen_mpi/ 006_footprint (base) [ehspector@milan2 5EEN]$ mkdir 007_virtualscreen (base) [ehspector@milan2 5EEN]$ mv 007_cartesian_min/ 008_cartesian_min (base) [ehspector@milan2 5EEN]$ mv 008_rescore/ 009_rescore (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt (base) [ehspector@milan2 5EEN]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 1O86 (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore (base) [ehspector@milan2 1O86]$ mv 006_virtual_screen_mpi/ 006_footprint (base) [ehspector@milan2 1O86]$ mkdir 007_virtualscreen (base) [ehspector@milan2 1O86]$ mv 007_cartesian_min/ 008_cartesian_min (base) [ehspector@milan2 1O86]$ mv 008_rescore/ 009_rescore (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd .. (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ vi commands.txt (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ bash commands.txt commands.txt: line 2: protein_name: Is a directory commands.txt: line 3: protein_name: Is a directory commands.txt: line 4: protein_name: Is a directory commands.txt: line 5: protein_name: Is a directory commands.txt: line 6: protein_name: Is a directory commands.txt: line 10: protein_name: Is a directory commands.txt: line 11: protein_name: Is a directory commands.txt: line 12: protein_name: Is a directory commands.txt: line 13: protein_name: Is a directory (base) [ehspector@milan2 AMS_536]$ ls 005_dock commands.txt flex protein_name Tutorials class_project fixed_anchor Notes.txt rigid (base) [ehspector@milan2 AMS_536]$ cd protein_name/ (base) [ehspector@milan2 protein_name]$ ls (base) [ehspector@milan2 protein_name]$ cd .. (base) [ehspector@milan2 AMS_536]$ rm protein_name/ rm: cannot remove 'protein_name/': Is a directory (base) [ehspector@milan2 AMS_536]$ rm -r protein_name/ (base) [ehspector@milan2 AMS_536]$ rm 005_dock (base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/ (base) [ehspector@milan2 AMS_536]$ rm -r flex/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt rigid Tutorials (base) [ehspector@milan2 AMS_536]$ rm -r rigid/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd .. (base) [ehspector@milan2 AMS_536]$ vi commands.txt (base) [ehspector@milan2 AMS_536]$ bash commands.txt (base) [ehspector@milan2 AMS_536]$ ls 001_structure 005_dock 009_rescore flex Tutorials 002_surface_spheres 006_footprint class_project Notes.txt 003_gridbox 007_virtualscreen commands.txt protein_name 004_energymin 008_cartesian_min fixed_anchor rigid (base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/ (base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/ (base) [ehspector@milan2 AMS_536]$ rm -r 003_surface_spheres/ rm: cannot remove '003_surface_spheres/': No such file or directory (base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/ (base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/ (base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/ (base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/ (base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/ (base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/ (base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/ (base) [ehspector@milan2 AMS_536]$ rm -r protein_name/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt fixed_anchor flex Notes.txt rigid Tutorials (base) [ehspector@milan2 AMS_536]$ rm -r flex (base) [ehspector@milan2 AMS_536]$ rm -r rigid/ (base) [ehspector@milan2 AMS_536]$ rm -r rigid/ rm: cannot remove 'rigid/': No such file or directory (base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/ (base) [ehspector@milan2 AMS_536]$ rm -r flex rm: cannot remove 'flex': No such file or directory (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ vi commands.txt (base) [ehspector@milan2 AMS_536]$ bash commands.txt mkdir: cannot create directory ‘protein_name’: File exists mkdir: cannot create directory ‘protein_name’: File exists (base) [ehspector@milan2 AMS_536]$ ls 001_structure 005_dock 009_rescore flex Tutorials 002_surface_spheres 006_footprint class_project Notes.txt 003_gridbox 007_virtualscreen commands.txt protein_name 004_energymin 008_cartesian_min fixed_anchor rigid (base) [ehspector@milan2 AMS_536]$ rm -r flex (base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/ (base) [ehspector@milan2 AMS_536]$ rm -r rigid/ (base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/ (base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/ (base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/ (base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/ (base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/ (base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/ (base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/ (base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/ (base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt protein_name Tutorials (base) [ehspector@milan2 AMS_536]$ cd protein_name/ (base) [ehspector@milan2 protein_name]$ ls (base) [ehspector@milan2 protein_name]$ cd .. (base) [ehspector@milan2 AMS_536]$ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 4 mix a100-[03-05,11] a100 up 8:00:00 3 alloc a100-[06,08,10] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 4 mix a100-[03-05,11] a100-large up 8:00:00 3 alloc a100-[06,08,10] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 4 mix a100-[03-05,11] a100-long up 2-00:00:00 3 alloc a100-[06,08,10] debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 9 mix dn[001,003-005,007,018,027,051,060] debug-40core up 1:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 9 mix dn[001,003-005,007,018,027,051,060] extended-40core up 7-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 9 mix dn[001,003-005,007,018,027,051,060] extended-40core-shared up 3-12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] extended-96core up 7-00:00:00 1 mix dg023 extended-96core up 7-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] extended-96core-shared up 3-12:00:00 1 mix dg023 extended-96core-shared up 3-12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048 hbm-1tb-long-96core up 2-00:00:00 2 alloc xm[045,047] hbm-1tb-long-96core up 2-00:00:00 1 idle xm046 hbm-extended-96core up 7-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 9 mix dn[001,003-005,007,018,027,051,060] large-40core up 8:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] large-96core up 8:00:00 1 mix dg023 large-96core up 8:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 9 mix dn[001,003-005,007,018,027,051,060] long-40core up 2-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 9 mix dn[001,003-005,007,018,027,051,060] long-40core-shared up 1-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] long-96core up 2-00:00:00 1 mix dg023 long-96core up 2-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] long-96core-shared up 1-00:00:00 1 mix dg023 long-96core-shared up 1-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 9 mix dn[001,003-005,007,018,027,051,060] medium-40core up 12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] medium-96core up 12:00:00 1 mix dg023 medium-96core up 12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060] short-40core up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060] short-40core-shared up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] short-96core up 4:00:00 1 mix dg023 short-96core up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] short-96core-shared up 4:00:00 1 mix dg023 short-96core-shared up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt protein_name Tutorials (base) [ehspector@milan2 AMS_536]$ rm -r protein_name (base) [ehspector@milan2 AMS_536]$ vi ~/.bashrc (base) [ehspector@milan2 AMS_536]$ source ~/.bashrc (base) [ehspector@milan2 AMS_536]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 4 mix a100-[03-05,11] a100 up 8:00:00 3 alloc a100-[06,08,10] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 4 mix a100-[03-05,11] a100-large up 8:00:00 3 alloc a100-[06,08,10] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 4 mix a100-[03-05,11] a100-long up 2-00:00:00 3 alloc a100-[06,08,10] debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 9 mix dn[001,003-005,007,018,027,051,060] debug-40core up 1:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 9 mix dn[001,003-005,007,018,027,051,060] extended-40core up 7-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 9 mix dn[001,003-005,007,018,027,051,060] extended-40core-shared up 3-12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] extended-96core up 7-00:00:00 1 mix dg023 extended-96core up 7-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] extended-96core-shared up 3-12:00:00 1 mix dg023 extended-96core-shared up 3-12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048 hbm-1tb-long-96core up 2-00:00:00 1 alloc xm047 hbm-1tb-long-96core up 2-00:00:00 2 idle xm[045-046] hbm-extended-96core up 7-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 9 mix dn[001,003-005,007,018,027,051,060] large-40core up 8:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] large-96core up 8:00:00 1 mix dg023 large-96core up 8:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 9 mix dn[001,003-005,007,018,027,051,060] long-40core up 2-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 9 mix dn[001,003-005,007,018,027,051,060] long-40core-shared up 1-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] long-96core up 2-00:00:00 1 mix dg023 long-96core up 2-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] long-96core-shared up 1-00:00:00 1 mix dg023 long-96core-shared up 1-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 9 mix dn[001,003-005,007,018,027,051,060] medium-40core up 12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] medium-96core up 12:00:00 1 mix dg023 medium-96core up 12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060] short-40core up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060] short-40core-shared up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] short-96core up 4:00:00 1 mix dg023 short-96core up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048] short-96core-shared up 4:00:00 1 mix dg023 short-96core-shared up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047] (base) [ehspector@milan2 AMS_536]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

(base) [ehspector@milan2 AMS_536]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP 5EEN % ls 5een.lig.min_scored.mol2 5een_noH_nocH.mol2 5een.pdb 5een_protein_only.pdb 5een.sph 5een_surface.dms 5een_H_cH.mol2 fad_scored.mol2 5een_ligand_H_cH.mol2 flex_scored.mol2 5een_ligand_noH_nocH.mol2 rigid_scored.mol2 5een_ligand_only.pdb selected_spheres.sph (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ home (base) [ehspector@milan1 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan1 espector]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/006_footprint/ (base) [ehspector@milan1 006_footprint]$ ls footprint.in foot.sh (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd (base) [ehspector@milan1 ~]$ cd ../../ (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/2025/transfers/ (base) [ehspector@milan1 transfers]$ ls 2025_02_12a_test.tar (base) [ehspector@milan1 transfers]$ cd .. (base) [ehspector@milan1 2025]$ ls 1EVE_DOCK_VS additional_files INSPH robbashrc_file rotations transfers (base) [ehspector@milan1 2025]$ cd transfers/ (base) [ehspector@milan1 transfers]$ pwd /gpfs/projects/AMS536/2025/transfers (base) [ehspector@milan1 transfers]$ ^C (base) [ehspector@milan1 transfers]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/transfers/2025_02_12a_test.tar . (base) [ehspector@milan1 Tutorials]$ ls 1O86 2025_02_12a_test.tar 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ mv 2025_02_12a_test.tar 2w26/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 003_gridbox 005_dock 007_virtual_screen 009_rescore Robs_2w26 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min 2025_02_12a_test.tar test4.tar (base) [ehspector@milan1 2w26]$ tar -xf 2025_02_12a_test.tar (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min 2W26 003_gridbox 006_footprint 009_rescore Robs_2w26 (base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_new_2w26 (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan1 Robs_new_2w26]$ ls 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1 (base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/ (base) [ehspector@milan1 005_analysis]$ ls 01fps_footprint_scored.txt 01fps_hbond_scored.txt 01fps.log1 01fps.out 01fps.sh 01fps_footprint_scored.txt.pdf 01fps.in 01fps.log2 01fps_scored.mol2 (base) [ehspector@milan1 005_analysis]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd .. (base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/005_analysis/01fps.in 006_footprint/footprint.in (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/005_analysis/ (base) [ehspector@milan1 005_analysis]$ vi 01fps (base) [ehspector@milan1 005_analysis]$ vi 01fps.sh (base) [ehspector@milan1 005_analysis]$ vi 01fps.sh (base) [ehspector@milan1 005_analysis]$ vi 01fps.sh (base) [ehspector@milan1 005_analysis]$ cd ../../006_footprint/ (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ vi footprint.sh (base) [ehspector@milan1 006_footprint]$ ls footprint.in foot.sh (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ cd ../001_structure/ (base) [ehspector@milan1 001_structure]$ ls 2w26_ligand_H_cH.mol2 2w26_ligand_noH_nocH.mol2 2w26_protein_H_cH.mol2 2w26_protein_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd ../006_footprint/ (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix footprint write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized

Molecule: 2w26.pdb

Elapsed time for docking:	0.008 seconds

Anchors:		1
Orientations:		1
Conformations:		1

         Footprint_Similarity_Score:            0.761241
                     FPS_vdw_energy:          -76.920898
                      FPS_es_energy:           -2.930423
                  FPS_vdw+es_energy:          -79.851318
                      FPS_num_hbond:                   2
                        FPS_vdw_fps:            0.642335
                         FPS_es_fps:            0.118906
                         FPS_hb_fps:            0.000000
                  FPS_vdw_fp_numres:                 286
                   FPS_es_fp_numres:                 286
                   FPS_hb_fp_numres:                 286

1 Molecules Processed Total elapsed time: 0.587 seconds Number of molecules per second: 1.705 Virtual memory used for this process: 80220 kilobytes Physical memory used for this process: 8192 kilobytes Traceback (most recent call last):

 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 9, in <module>
   import matplotlib

ModuleNotFoundError: No module named 'matplotlib' (base) [ehspector@milan1 006_footprint]$ module load python (base) [ehspector@milan1 006_footprint]$ module list Currently Loaded Modulefiles:

1) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack      
2) shared                   4) mvapich2/gcc13.2/2.3.7   6) python/3.11.2

(base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix footprint write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized

Molecule: 2w26.pdb

Elapsed time for docking:	0.008 seconds

Anchors:		1
Orientations:		1
Conformations:		1

         Footprint_Similarity_Score:            0.761241
                     FPS_vdw_energy:          -76.920898
                      FPS_es_energy:           -2.930423
                  FPS_vdw+es_energy:          -79.851318
                      FPS_num_hbond:                   2
                        FPS_vdw_fps:            0.642335
                         FPS_es_fps:            0.118906
                         FPS_hb_fps:            0.000000
                  FPS_vdw_fp_numres:                 286
                   FPS_es_fp_numres:                 286
                   FPS_hb_fp_numres:                 286

1 Molecules Processed Total elapsed time: 0.487 seconds Number of molecules per second: 2.053 Virtual memory used for this process: 80224 kilobytes Physical memory used for this process: 8192 kilobytes Traceback (most recent call last):

 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
   main()
 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
   (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
   fp_file = open(filename,'r')
             ^^^^^^^^^^^^^^^^^^

FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt' (base) [ehspector@milan1 006_footprint]$ ls footprint_footprint_scored.txt footprint_hbond_scored.txt footprint.in footprint_scored.mol2 foot.sh (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix 2w26 write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized

Molecule: 2w26.pdb

Elapsed time for docking:	0.008 seconds

Anchors:		1
Orientations:		1
Conformations:		1

         Footprint_Similarity_Score:            0.761241
                     FPS_vdw_energy:          -76.920898
                      FPS_es_energy:           -2.930423
                  FPS_vdw+es_energy:          -79.851318
                      FPS_num_hbond:                   2
                        FPS_vdw_fps:            0.642335
                         FPS_es_fps:            0.118906
                         FPS_hb_fps:            0.000000
                  FPS_vdw_fp_numres:                 286
                   FPS_es_fp_numres:                 286
                   FPS_hb_fp_numres:                 286

1 Molecules Processed Total elapsed time: 0.525 seconds Number of molecules per second: 1.905 Virtual memory used for this process: 80224 kilobytes Physical memory used for this process: 8192 kilobytes Traceback (most recent call last):

 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
   main()
 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
   (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
   fp_file = open(filename,'r')
             ^^^^^^^^^^^^^^^^^^

FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt' (base) [ehspector@milan1 006_footprint]$ ls 2w26_footprint_scored.txt footprint_footprint_scored.txt footprint_scored.mol2 2w26_hbond_scored.txt footprint_hbond_scored.txt foot.sh 2w26_scored.mol2 footprint.in (base) [ehspector@milan1 006_footprint]$ rm *mol2 (base) [ehspector@milan1 006_footprint]$ ls 2w26_footprint_scored.txt footprint_footprint_scored.txt footprint.in 2w26_hbond_scored.txt footprint_hbond_scored.txt foot.sh (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ rm *.txt (base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix 2w26 write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized Warning: atom type Ca in Fingerprint::return_atom_type not recognized

Molecule: 2w26.pdb

Elapsed time for docking:	0.008 seconds

Anchors:		1
Orientations:		1
Conformations:		1

         Footprint_Similarity_Score:            0.761241
                     FPS_vdw_energy:          -76.920898
                      FPS_es_energy:           -2.930423
                  FPS_vdw+es_energy:          -79.851318
                      FPS_num_hbond:                   2
                        FPS_vdw_fps:            0.642335
                         FPS_es_fps:            0.118906
                         FPS_hb_fps:            0.000000
                  FPS_vdw_fp_numres:                 286
                   FPS_es_fp_numres:                 286
                   FPS_hb_fp_numres:                 286

1 Molecules Processed Total elapsed time: 0.585 seconds Number of molecules per second: 1.710 Virtual memory used for this process: 80224 kilobytes Physical memory used for this process: 8192 kilobytes No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument. /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.

 plt.show()

(base) [ehspector@milan1 006_footprint]$ ls 2w26_footprint_scored.txt 2w26_hbond_scored.txt footprint.in 2w26_footprint_scored.txt.pdf 2w26_scored.mol2 foot.sh (base) [ehspector@milan1 006_footprint]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan1 Robs_new_2w26]$ ls 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1 (base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/ (base) [ehspector@milan1 005_analysis]$ ls 01fps_footprint_scored.txt 01fps_hbond_scored.txt 01fps.log1 01fps.out 01fps.sh 01fps_footprint_scored.txt.pdf 01fps.in 01fps.log2 01fps_scored.mol2 (base) [ehspector@milan1 005_analysis]$ cd ../006_ga_lib/ (base) [ehspector@milan1 006_ga_lib]$ ls 01lib.sh 2W26.fraglib.out 2W26_fragout_scored.mol2 02combine.sh 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26.fraglib.in 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 unique_full_sorted_fraglib.dat 2W26.fraglib.log 2W26_fraglib_torenv.dat (base) [ehspector@milan1 006_ga_lib]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan1 Robs_new_2w26]$ ls 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1 (base) [ehspector@milan1 Robs_new_2w26]$ cd 000_test/ (base) [ehspector@milan1 000_test]$ ls test_dock.in (base) [ehspector@milan1 000_test]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/ (base) [ehspector@milan1 004_dock]$ ls 01min.in 02rgd.in 03fad.in 04flx.in 05vs.out 01min.log 02rgd.log 03fad.log 04flx.log 05vs_scored.mol2 01min.out 02rgd.out 03fad.out 04flx.out 05vs.sh 01min_scored.mol2 02rgd_scored.mol2 03fad_scored.mol2 04flx.sh 05vs_slurm 01min.sh 02rgd.sh 03fad.sh 05vs.in VS_library_005.mol2 (base) [ehspector@milan1 004_dock]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd .. (base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/004_dock/05vs.in 007_virtual_screen/ (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan1 007_virtual_screen]$ ls 05vs.in (base) [ehspector@milan1 007_virtual_screen]$ mv 05vs.in virtual.in (base) [ehspector@milan1 007_virtual_screen]$ ls virtual.in (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in (base) [ehspector@milan1 007_virtual_screen]$ cd (base) [ehspector@milan1 ~]$ cd ../../ (base) [ehspector@milan1 gpfs]$ cd AMS536 -bash: cd: AMS536: No such file or directory (base) [ehspector@milan1 gpfs]$ cd projects/AMS536 (base) [ehspector@milan1 AMS536]$ ls 1EVE_Lig_nH.mol2 1eve_Rec_nH.mol2 2018 2021 2024 junk.txt 1EVE_Lig_wH.mol2 1eve_Rec_wH.mol2 2019 2022 2025 zzz.anchors 1EVE_Rec_nHDMS.dms 2017 2020 2023 get_anchors.py zzz.programs (base) [ehspector@milan1 AMS536]$ cd 2025 (base) [ehspector@milan1 2025]$ cd .. (base) [ehspector@milan1 AMS536]$ cd zzz.programs/ (base) [ehspector@milan1 zzz.programs]$ ls amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber dock6.10 dock6.12 gen-frags-12 VS_libraries dock6.10_milan dock6.12_ams536 old (base) [ehspector@milan1 zzz.programs]$ cd VS_libraries/ (base) [ehspector@milan1 VS_libraries]$ ls VS_library_100.mol2 VS_library_25K.mol2 VS_library_5K.mol2 (base) [ehspector@milan1 VS_libraries]$ pwd /gpfs/projects/AMS536/zzz.programs/VS_libraries (base) [ehspector@milan1 VS_libraries]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in (base) [ehspector@milan1 007_virtual_screen]$ cd ../006_footprint/ (base) [ehspector@milan1 006_footprint]$ ls 2w26_footprint_scored.txt 2w26_hbond_scored.txt footprint.in 2w26_footprint_scored.txt.pdf 2w26_scored.mol2 foot.sh (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ cd ../007_virtual_screen/ (base) [ehspector@milan1 007_virtual_screen]$ ls virtual.in (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm (base) [ehspector@milan1 007_virtual_screen]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan1 Robs_new_2w26]$ ls 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1 (base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/ (base) [ehspector@milan1 005_analysis]$ ls 01fps_footprint_scored.txt 01fps_hbond_scored.txt 01fps.log1 01fps.out 01fps.sh 01fps_footprint_scored.txt.pdf 01fps.in 01fps.log2 01fps_scored.mol2 (base) [ehspector@milan1 005_analysis]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/ (base) [ehspector@milan1 004_dock]$ ls 01min.in 02rgd.in 03fad.in 04flx.in 05vs.out 01min.log 02rgd.log 03fad.log 04flx.log 05vs_scored.mol2 01min.out 02rgd.out 03fad.out 04flx.out 05vs.sh 01min_scored.mol2 02rgd_scored.mol2 03fad_scored.mol2 04flx.sh 05vs_slurm 01min.sh 02rgd.sh 03fad.sh 05vs.in VS_library_005.mol2 (base) [ehspector@milan1 004_dock]$ vi 05vs.sh (base) [ehspector@milan1 004_dock]$ vi 05vs.sh (base) [ehspector@milan1 004_dock]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan1 007_virtual_screen]$ ls virtual.in virtual.slurm (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm (base) [ehspector@milan1 007_virtual_screen]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 4 mix a100-[03-05,11] a100 up 8:00:00 3 alloc a100-[06,08,10] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 4 mix a100-[03-05,11] a100-large up 8:00:00 3 alloc a100-[06,08,10] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 4 mix a100-[03-05,11] a100-long up 2-00:00:00 3 alloc a100-[06,08,10] debug-40core up 1:00:00 3 plnd dn[032,040,049] debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 8 mix dn[001,003-005,007,018,027,051] debug-40core up 1:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] extended-40core up 7-00:00:00 3 plnd dn[032,040,049] extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 8 mix dn[001,003-005,007,018,027,051] extended-40core up 7-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] extended-40core-shared up 3-12:00:00 3 plnd dn[032,040,049] extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 8 mix dn[001,003-005,007,018,027,051] extended-40core-shared up 3-12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] extended-96core up 7-00:00:00 1 mix dg023 extended-96core up 7-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] extended-96core-shared up 3-12:00:00 1 mix dg023 extended-96core-shared up 3-12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048 hbm-1tb-long-96core up 2-00:00:00 1 alloc xm045 hbm-1tb-long-96core up 2-00:00:00 2 idle xm[046-047] hbm-extended-96core up 7-00:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 3 plnd dn[032,040,049] large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 8 mix dn[001,003-005,007,018,027,051] large-40core up 8:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] large-96core up 8:00:00 1 mix dg023 large-96core up 8:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] long-40core up 2-00:00:00 3 plnd dn[032,040,049] long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 8 mix dn[001,003-005,007,018,027,051] long-40core up 2-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] long-40core-shared up 1-00:00:00 3 plnd dn[032,040,049] long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 8 mix dn[001,003-005,007,018,027,051] long-40core-shared up 1-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] long-96core up 2-00:00:00 1 mix dg023 long-96core up 2-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] long-96core-shared up 1-00:00:00 1 mix dg023 long-96core-shared up 1-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] medium-40core up 12:00:00 3 plnd dn[032,040,049] medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 8 mix dn[001,003-005,007,018,027,051] medium-40core up 12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] medium-96core up 12:00:00 1 mix dg023 medium-96core up 12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] ood-short-96core up 4:00:00 1 alloc dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 3 plnd dn[032,040,049] short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 8 mix dn[001,003-005,007,018,027,051] short-40core up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] short-40core-shared up 4:00:00 3 plnd dn[032,040,049] short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 8 mix dn[001,003-005,007,018,027,051] short-40core-shared up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] short-96core up 4:00:00 1 mix dg023 short-96core up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] short-96core-shared up 4:00:00 1 mix dg023 short-96core-shared up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm (base) [ehspector@milan1 007_virtual_screen]$ ls virtual.in virtual.slurm (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.slurm sbatch: error: QOSMaxNodePerJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits) (base) [ehspector@milan1 007_virtual_screen]$ mv virtual.slurm virtual.sh (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh sbatch: error: QOSMaxNodePerJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits) (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh Submitted batch job 927425 (base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan1 007_virtual_screen]$ (base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan1 007_virtual_screen]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan1 ~]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 4 mix a100-[03-05,11] a100 up 8:00:00 3 alloc a100-[06,08,10] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 4 mix a100-[03-05,11] a100-large up 8:00:00 3 alloc a100-[06,08,10] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 4 mix a100-[03-05,11] a100-long up 2-00:00:00 3 alloc a100-[06,08,10] debug-40core up 1:00:00 3 plnd dn[032,040,049] debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 8 mix dn[001,003-005,007,018,027,051] debug-40core up 1:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] extended-40core up 7-00:00:00 3 plnd dn[032,040,049] extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 8 mix dn[001,003-005,007,018,027,051] extended-40core up 7-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] extended-40core-shared up 3-12:00:00 3 plnd dn[032,040,049] extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 8 mix dn[001,003-005,007,018,027,051] extended-40core-shared up 3-12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] extended-96core up 7-00:00:00 1 mix dg023 extended-96core up 7-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] extended-96core-shared up 3-12:00:00 1 mix dg023 extended-96core-shared up 3-12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048 hbm-1tb-long-96core up 2-00:00:00 1 alloc xm045 hbm-1tb-long-96core up 2-00:00:00 2 idle xm[046-047] hbm-extended-96core up 7-00:00:00 2 plnd xm[008,094] hbm-extended-96core up 7-00:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093] hbm-large-96core up 8:00:00 2 plnd xm[008,094] hbm-large-96core up 8:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093] hbm-long-96core up 2-00:00:00 2 plnd xm[008,094] hbm-long-96core up 2-00:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093] hbm-medium-96core up 12:00:00 2 plnd xm[008,094] hbm-medium-96core up 12:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093] hbm-short-96core up 4:00:00 2 plnd xm[008,094] hbm-short-96core up 4:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093] large-40core up 8:00:00 3 plnd dn[032,040,049] large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 8 mix dn[001,003-005,007,018,027,051] large-40core up 8:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] large-96core up 8:00:00 1 mix dg023 large-96core up 8:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] long-40core up 2-00:00:00 3 plnd dn[032,040,049] long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 8 mix dn[001,003-005,007,018,027,051] long-40core up 2-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] long-40core-shared up 1-00:00:00 3 plnd dn[032,040,049] long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 8 mix dn[001,003-005,007,018,027,051] long-40core-shared up 1-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] long-96core up 2-00:00:00 1 mix dg023 long-96core up 2-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] long-96core-shared up 1-00:00:00 1 mix dg023 long-96core-shared up 1-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] medium-40core up 12:00:00 3 plnd dn[032,040,049] medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 8 mix dn[001,003-005,007,018,027,051] medium-40core up 12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] medium-96core up 12:00:00 1 mix dg023 medium-96core up 12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 3 plnd dn[032,040,049] short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 8 mix dn[001,003-005,007,018,027,051] short-40core up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] short-40core-shared up 4:00:00 3 plnd dn[032,040,049] short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 8 mix dn[001,003-005,007,018,027,051] short-40core-shared up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] short-96core up 4:00:00 1 mix dg023 short-96core up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044] short-96core-shared up 4:00:00 1 mix dg023 short-96core-shared up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048] (base) [ehspector@milan1 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927425 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan1 2w26]$ scancel 927425 (base) [ehspector@milan1 2w26]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan1 007_virtual_screen]$ ls virtual.in virtual.sh (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh Submitted batch job 927435 (base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 007_virtual_screen]$ cd .. (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 5EEN/006_footprint/footprint.in (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 5EEN/006_footprint/foot.sh (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 1O86/006_footprint/foot.sh (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 1O86/006_footprint/footprint.in (base) [ehspector@milan1 Tutorials]$ cd 5EEN/006_footprint/ (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ module load python (base) [ehspector@milan1 006_footprint]$ cd ../001_structure/ (base) [ehspector@milan1 001_structure]$ ls 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd ../006_footprint/ (base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/5een.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/5een_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/5een_protein_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix 5een write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

Error Opening Receptor File! Traceback (most recent call last):

 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
   main()
 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
   (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 56, in identify_residues
   resindex_selected.append(fp_array[(num_res-1)-i][0])
                            12:36, 21 February 2025 (EST)Stonybrook (talk)^^^^^^^^^^^^^^^

IndexError: list index out of range (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/5een.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/5een_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/5een_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix 5een write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 3018 WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5500 WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5501 Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type K in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized

Molecule: 5een.pdb

Elapsed time for docking:	0.008 seconds

Anchors:		1
Orientations:		1
Conformations:		1

         Footprint_Similarity_Score:           10.378089
                     FPS_vdw_energy:          -39.542568
                      FPS_es_energy:          -11.422824
                  FPS_vdw+es_energy:          -50.965393
                      FPS_num_hbond:                   2
                        FPS_vdw_fps:            8.225544
                         FPS_es_fps:            2.152545
                         FPS_hb_fps:            0.000000
                  FPS_vdw_fp_numres:                 362
                   FPS_es_fp_numres:                 362
                   FPS_hb_fp_numres:                 362

1 Molecules Processed Total elapsed time: 0.778 seconds Number of molecules per second: 1.285 Virtual memory used for this process: 80616 kilobytes Physical memory used for this process: 9196 kilobytes No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument. /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.

 plt.show()

(base) [ehspector@milan1 006_footprint]$ ls 5een_footprint_scored.txt 5een_hbond_scored.txt footprint.in 5een_footprint_scored.txt.pdf 5een_scored.mol2 foot.sh (base) [ehspector@milan1 006_footprint]$ cd .. (base) [ehspector@milan1 5EEN]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd 1O86/001_structure/ (base) [ehspector@milan1 001_structure]$ ls 1O86_ligand_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_H_cH.mol2 1O86_protein_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd ../006_footprint/ (base) [ehspector@milan1 006_footprint]$ vi footprint.in (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ vi foot.sh (base) [ehspector@milan1 006_footprint]$ bash foot.sh

DOCK v6.12

Released September 2024 Copyright UCSF

Conformational Sampling Parameters

conformer_search_type rigid

Internal Energy Parameters

use_internal_energy no

Molecule Library Input Parameters

ligand_atom_file ../004_energymin/1O86.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no

Database Filter Parameters

use_database_filter no

Orient Ligand Parameters

orient_ligand no

Bump Filter Parameters

bump_filter no

Master Score Parameters

score_molecules yes

Contact Score Parameters

contact_score_primary no

Grid Score Parameters

grid_score_primary no

GIST Score Parameters

gist_score_primary no

MultiGrid Score Parameters

multigrid_score_primary no

Dock3.5 Score Parameters

dock3.5_score_primary no

Continuous Energy Score Parameters

continuous_score_primary no

Footprint Similarity Score Parameters

footprint_similarity_score_primary yes fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001_structure/1O86_ligand_H_cH.mol2 fps_score_foot_compare_type Euclidean

You chose to use the Euclidean distance as the metric to compare the footprints. When the value is 0 then there is perfect agreement between the two footprints. As the agreement gets worse between the two footprints the value increases.

fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001_structure/1O86_protein_H_cH.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

minimize_ligand no simplex_final_min no

Atom Typing Parameters

atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Molecule Library Output Parameters

ligand_outfile_prefix 1O86 write_mol_solvation no write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 score_threshold 100.0 rank_ligands no

Initializing Library File Routines...

To cite Footprint Similarity Score use:

Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.

Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized Warning: atom type Zn in Fingerprint::return_atom_type not recognized

Molecule: 1O86_ligand.pdb

Elapsed time for docking:	0.019 seconds

Anchors:		1
Orientations:		1
Conformations:		1

         Footprint_Similarity_Score:           19.990522
                     FPS_vdw_energy:          -62.449921
                      FPS_es_energy:          -49.059299
                  FPS_vdw+es_energy:         -111.509216
                      FPS_num_hbond:                   4
                        FPS_vdw_fps:            4.596808
                         FPS_es_fps:           15.393714
                         FPS_hb_fps:            1.000000
                  FPS_vdw_fp_numres:                 582
                   FPS_es_fp_numres:                 582
                   FPS_hb_fp_numres:                 582

1 Molecules Processed Total elapsed time: 2.107 seconds Number of molecules per second: 0.475 Virtual memory used for this process: 83536 kilobytes Physical memory used for this process: 11424 kilobytes No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument. /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.

 plt.show()

(base) [ehspector@milan1 006_footprint]$ ls 1O86_footprint_scored.txt 1O86_hbond_scored.txt footprint.in 1O86_footprint_scored.txt.pdf 1O86_scored.mol2 foot.sh (base) [ehspector@milan1 006_footprint]$ cd .. (base) [ehspector@milan1 1O86]$ cd .. (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 5EEN/007_virtualscreen/virtual.in (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 5EEN/007_virtualscreen/virtual.sh (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 1O86/007_virtualscreen/virtual.sh (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 1O86/007_virtualscreen/virtual.in (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan2 ~]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 2 mix a100-[03,05] a100 up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 2 mix a100-[03,05] a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 2 mix a100-[03,05] a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11] debug-40core up 1:00:00 3 plnd dn[050,061-062] debug-40core up 1:00:00 6 alloc@ dn[009,026,029,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 4 mix dn[004-005,018,051] debug-40core up 1:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] extended-40core up 7-00:00:00 3 plnd dn[050,061-062] extended-40core up 7-00:00:00 6 alloc@ dn[009,026,029,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 4 mix dn[004-005,018,051] extended-40core up 7-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] extended-40core-shared up 3-12:00:00 3 plnd dn[050,061-062] extended-40core-shared up 3-12:00:00 6 alloc@ dn[009,026,029,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 4 mix dn[004-005,018,051] extended-40core-shared up 3-12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core up 7-00:00:00 2 mix dg[009,023] extended-96core up 7-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] extended-96core up 7-00:00:00 3 idle dg[032,035-036] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core-shared up 3-12:00:00 2 mix dg[009,023] extended-96core-shared up 3-12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] extended-96core-shared up 3-12:00:00 3 idle dg[032,035-036] hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047] hbm-1tb-long-96core up 2-00:00:00 1 idle xm048 hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 3 plnd dn[050,061-062] large-40core up 8:00:00 6 alloc@ dn[009,026,029,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 4 mix dn[004-005,018,051] large-40core up 8:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043] large-96core up 8:00:00 2 mix dg[009,023] large-96core up 8:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] large-96core up 8:00:00 3 idle dg[032,035-036] long-40core up 2-00:00:00 3 plnd dn[050,061-062] long-40core up 2-00:00:00 6 alloc@ dn[009,026,029,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 4 mix dn[004-005,018,051] long-40core up 2-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] long-40core-shared up 1-00:00:00 3 plnd dn[050,061-062] long-40core-shared up 1-00:00:00 6 alloc@ dn[009,026,029,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 4 mix dn[004-005,018,051] long-40core-shared up 1-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core up 2-00:00:00 2 mix dg[009,023] long-96core up 2-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] long-96core up 2-00:00:00 3 idle dg[032,035-036] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core-shared up 1-00:00:00 2 mix dg[009,023] long-96core-shared up 1-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] long-96core-shared up 1-00:00:00 3 idle dg[032,035-036] medium-40core up 12:00:00 3 plnd dn[050,061-062] medium-40core up 12:00:00 6 alloc@ dn[009,026,029,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 4 mix dn[004-005,018,051] medium-40core up 12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] medium-96core up 12:00:00 2 mix dg[009,023] medium-96core up 12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] medium-96core up 12:00:00 3 idle dg[032,035-036] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 3 plnd dn[050,061-062] short-40core up 4:00:00 6 alloc@ dn[009,026,029,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 4 mix dn[004-005,018,051] short-40core up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] short-40core-shared up 4:00:00 3 plnd dn[050,061-062] short-40core-shared up 4:00:00 6 alloc@ dn[009,026,029,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 4 mix dn[004-005,018,051] short-40core-shared up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core up 4:00:00 2 mix dg[009,023] short-96core up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] short-96core up 4:00:00 3 idle dg[032,035-036] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core-shared up 4:00:00 2 mix dg[009,023] short-96core-shared up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048] short-96core-shared up 4:00:00 3 idle dg[032,035-036] (base) [ehspector@milan2 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           927435 ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)

(base) [ehspector@milan2 ~]$ scancel 927435 (base) [ehspector@milan2 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh (base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh Submitted batch job 928050 (base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928050 short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtual_screen]$ scancel 928050 (base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh (base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh Submitted batch job 928053 (base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       0:03      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       0:07      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       0:10      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       0:49      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtual_screen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       0:50      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtual_screen]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       1:42      3 dg[032,035-036]

(base) [ehspector@milan2 Tutorials]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       1:43      3 dg[032,035-036]

(base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/ (base) [ehspector@milan2 006_footprint]$ ls 2w26_footprint_scored.txt 2w26_hbond_scored.txt footprint.in 2w26_footprint_scored.txt.pdf 2w26_scored.mol2 foot.sh (base) [ehspector@milan2 006_footprint]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       6:28      3 dg[032,035-036]

(base) [ehspector@milan2 006_footprint]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       6:29      3 dg[032,035-036]

(base) [ehspector@milan2 006_footprint]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       6:56      3 dg[032,035-036]

(base) [ehspector@milan2 006_footprint]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R       7:42      3 dg[032,035-036]

(base) [ehspector@milan2 006_footprint]$ cd .. (base) [ehspector@milan2 2w26]$ cd ../5EEN/ (base) [ehspector@milan2 5EEN]$ ls 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt (base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/ (base) [ehspector@milan2 007_virtualscreen]$ ls virtual.in virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 2 mix a100-[03,05] a100 up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 2 mix a100-[03,05] a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 2 mix a100-[03,05] a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11] debug-40core up 1:00:00 3 plnd dn[050,061-062] debug-40core up 1:00:00 6 alloc@ dn[009,026,029,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 4 mix dn[004-005,018,051] debug-40core up 1:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] extended-40core up 7-00:00:00 3 plnd dn[050,061-062] extended-40core up 7-00:00:00 6 alloc@ dn[009,026,029,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 4 mix dn[004-005,018,051] extended-40core up 7-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] extended-40core-shared up 3-12:00:00 3 plnd dn[050,061-062] extended-40core-shared up 3-12:00:00 6 alloc@ dn[009,026,029,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 4 mix dn[004-005,018,051] extended-40core-shared up 3-12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] extended-96core up 7-00:00:00 1 plnd dg039 extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core up 7-00:00:00 2 mix dg[009,023] extended-96core up 7-00:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] extended-96core-shared up 3-12:00:00 1 plnd dg039 extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core-shared up 3-12:00:00 2 mix dg[009,023] extended-96core-shared up 3-12:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047] hbm-1tb-long-96core up 2-00:00:00 1 idle xm048 hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 3 plnd dn[050,061-062] large-40core up 8:00:00 6 alloc@ dn[009,026,029,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 4 mix dn[004-005,018,051] large-40core up 8:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] large-96core up 8:00:00 1 plnd dg039 large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043] large-96core up 8:00:00 2 mix dg[009,023] large-96core up 8:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] long-40core up 2-00:00:00 3 plnd dn[050,061-062] long-40core up 2-00:00:00 6 alloc@ dn[009,026,029,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 4 mix dn[004-005,018,051] long-40core up 2-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] long-40core-shared up 1-00:00:00 3 plnd dn[050,061-062] long-40core-shared up 1-00:00:00 6 alloc@ dn[009,026,029,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 4 mix dn[004-005,018,051] long-40core-shared up 1-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] long-96core up 2-00:00:00 1 plnd dg039 long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core up 2-00:00:00 2 mix dg[009,023] long-96core up 2-00:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] long-96core-shared up 1-00:00:00 1 plnd dg039 long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core-shared up 1-00:00:00 2 mix dg[009,023] long-96core-shared up 1-00:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] medium-40core up 12:00:00 3 plnd dn[050,061-062] medium-40core up 12:00:00 6 alloc@ dn[009,026,029,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 4 mix dn[004-005,018,051] medium-40core up 12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] medium-96core up 12:00:00 1 plnd dg039 medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] medium-96core up 12:00:00 2 mix dg[009,023] medium-96core up 12:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 3 plnd dn[050,061-062] short-40core up 4:00:00 6 alloc@ dn[009,026,029,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 4 mix dn[004-005,018,051] short-40core up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] short-40core-shared up 4:00:00 3 plnd dn[050,061-062] short-40core-shared up 4:00:00 6 alloc@ dn[009,026,029,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 4 mix dn[004-005,018,051] short-40core-shared up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060] short-96core up 4:00:00 1 plnd dg039 short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core up 4:00:00 2 mix dg[009,023] short-96core up 4:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] short-96core-shared up 4:00:00 1 plnd dg039 short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core-shared up 4:00:00 2 mix dg[009,023] short-96core-shared up 4:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048] (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.in (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928057 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      12:28      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      12:41      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      12:46      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      12:47      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      12:49      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      14:35      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      14:38      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      14:40      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      14:42      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ ls virtual.in virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      15:00      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928057 short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      15:06      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ scancel 928057 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928053 short-96c 2w26_vs_ ehspecto  R      16:00      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 2 mix a100-[03,05] a100 up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 2 mix a100-[03,05] a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 2 mix a100-[03,05] a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11] debug-40core up 1:00:00 2 plnd dn[061-062] debug-40core up 1:00:00 6 alloc@ dn[009,026,029,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 4 mix dn[004-005,018,051] debug-40core up 1:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] extended-40core up 7-00:00:00 2 plnd dn[061-062] extended-40core up 7-00:00:00 6 alloc@ dn[009,026,029,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 4 mix dn[004-005,018,051] extended-40core up 7-00:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] extended-40core-shared up 3-12:00:00 2 plnd dn[061-062] extended-40core-shared up 3-12:00:00 6 alloc@ dn[009,026,029,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 4 mix dn[004-005,018,051] extended-40core-shared up 3-12:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] extended-96core up 7-00:00:00 3 plnd dg[006,026,039] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core up 7-00:00:00 2 mix dg[009,023] extended-96core up 7-00:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] extended-96core-shared up 3-12:00:00 3 plnd dg[006,026,039] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core-shared up 3-12:00:00 2 mix dg[009,023] extended-96core-shared up 3-12:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047] hbm-1tb-long-96core up 2-00:00:00 1 idle xm048 hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 2 plnd dn[061-062] large-40core up 8:00:00 6 alloc@ dn[009,026,029,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 4 mix dn[004-005,018,051] large-40core up 8:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] large-96core up 8:00:00 3 plnd dg[006,026,039] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043] large-96core up 8:00:00 2 mix dg[009,023] large-96core up 8:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] long-40core up 2-00:00:00 2 plnd dn[061-062] long-40core up 2-00:00:00 6 alloc@ dn[009,026,029,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 4 mix dn[004-005,018,051] long-40core up 2-00:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] long-40core-shared up 1-00:00:00 2 plnd dn[061-062] long-40core-shared up 1-00:00:00 6 alloc@ dn[009,026,029,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 4 mix dn[004-005,018,051] long-40core-shared up 1-00:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] long-96core up 2-00:00:00 3 plnd dg[006,026,039] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core up 2-00:00:00 2 mix dg[009,023] long-96core up 2-00:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] long-96core-shared up 1-00:00:00 3 plnd dg[006,026,039] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core-shared up 1-00:00:00 2 mix dg[009,023] long-96core-shared up 1-00:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] medium-40core up 12:00:00 2 plnd dn[061-062] medium-40core up 12:00:00 6 alloc@ dn[009,026,029,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 4 mix dn[004-005,018,051] medium-40core up 12:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] medium-96core up 12:00:00 3 plnd dg[006,026,039] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] medium-96core up 12:00:00 2 mix dg[009,023] medium-96core up 12:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 2 plnd dn[061-062] short-40core up 4:00:00 6 alloc@ dn[009,026,029,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 4 mix dn[004-005,018,051] short-40core up 4:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] short-40core-shared up 4:00:00 2 plnd dn[061-062] short-40core-shared up 4:00:00 6 alloc@ dn[009,026,029,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 4 mix dn[004-005,018,051] short-40core-shared up 4:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060] short-96core up 4:00:00 3 plnd dg[006,026,039] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core up 4:00:00 2 mix dg[009,023] short-96core up 4:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] short-96core-shared up 4:00:00 3 plnd dg[006,026,039] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core-shared up 4:00:00 2 mix dg[009,023] short-96core-shared up 4:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048] (base) [ehspector@milan2 007_virtualscreen]$ cd ../ (base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/ (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928060 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      19:15      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      19:17      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      19:18      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      19:19      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      19:38      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      19:40      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      19:41      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928063 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928063 short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      21:35      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ scancel 928063 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      21:54      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh sbatch: error: QOSMaxNodePerJobLimit sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits) (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928066 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:11      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:13      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:13      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:16      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:17      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:17      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      23:18      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      24:32      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      24:38      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      24:39      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928070 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      25:10      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
           928053 short-96c 2w26_vs_ ehspecto  R      25:19      3 dg[032,035-036]
           928066 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

(base) [ehspector@milan2 007_virtualscreen]$ scancel 928066 (base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      25:37      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      25:50      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928053 short-96c 2w26_vs_ ehspecto  R      25:51      3 dg[032,035-036]

(base) [ehspector@milan2 007_virtualscreen]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@login.seawulf.stonybrook.edu ehspector@login.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in...

- - - IMPORTANT MESSAGE BELOW****

In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.

(base) [ehspector@login2 ~]$ cd .. (base) [ehspector@login2 home]$ home (base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd ../../install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c amake[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock\ > ^C (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Thu Feb 13 11:05:05 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:778:5: error: ‘Filter’ was not declared in this scope

 778 |     Filter filter;
     |     ^12:36, 21 February 2025 (EST)

make[1]: *** [dockmol.o] Error 1 make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [dock] Error 2 (base) [ehspector@login2 install]$ cd ../../ (base) [ehspector@login2 builds]$ cd alpha_branch/src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd ../../ (base) [ehspector@login2 alpha_branch]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

(base) [ehspector@login2 alpha_branch]$ cd install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Thu Feb 13 11:07:50 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp g++ -c -O2 -std=c++11 -o filter.o filter.cpp g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp g++ -c -O2 -std=c++11 -o grid.o grid.cpp g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp g++ -c -O2 -std=c++11 -o orient.o orient.cpp g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp g++ -c -O2 -std=c++11 -o score.o score.cpp g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -o trace.o trace.cpp g++ -c -O2 -std=c++11 -o utils.o utils.cpp g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp cd nab && make all make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -lm -lpthread mv dock6 ../../bin make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 (base) [ehspector@login2 install]$ cd ../ (base) [ehspector@login2 alpha_branch]$ cd ../ (base) [ehspector@login2 builds]$ cd alpha_branch/src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd .. (base) [ehspector@login2 src]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Thu Feb 13 11:20:49 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘gasteiger’; did you mean ‘gasteigerize’?

 917 |     if (filter.gasteiger){
     |                ^12:36, 21 February 2025 (EST)Stonybrook (talk)
     |                gasteigerize

dockmol.cpp:931:5: error: jump to label ‘skip’

 931 |     skip:
     |     ^Stonybrook (talk)

dockmol.cpp:918:10: note: from here

 918 |     goto skip;
     |          ^Stonybrook (talk)

dockmol.cpp:919:9: note: crosses initialization of ‘int num_zeros’

 919 |     int num_zeros = 0;
     |         ^12:36, 21 February 2025 (EST)Stonybrook (talk)

make[1]: *** [dockmol.o] Error 1 make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [dock] Error 2 (base) [ehspector@login2 install]$ cd .. (base) [ehspector@login2 alpha_branch]$ cd src/dock (base) [ehspector@login2 dock]$ vi dockmol.cpp (base) [ehspector@login2 dock]$ cd .. \(base) [ehspector@login2 src]$ cd ../ (base) [ehspector@login2 alpha_branch]$ cd install/ (base) [ehspector@login2 install]$ make clean make -C ../src clean make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@login2 install]$ make dock Starting installation of DOCK v6.12 program dock at Thu Feb 13 11:25:35 EST 2025.

make -C ../src/dock install make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp g++ -c -O2 -std=c++11 -o dock.o dock.cpp g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp g++ -c -O2 -std=c++11 -o filter.o filter.cpp g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp g++ -c -O2 -std=c++11 -o grid.o grid.cpp g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp g++ -c -O2 -std=c++11 -o orient.o orient.cpp g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp g++ -c -O2 -std=c++11 -o score.o score.cpp g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -o trace.o trace.cpp g++ -c -O2 -std=c++11 -o utils.o utils.cpp g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp cd nab && make all make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -lm -lpthread mv dock6 ../../bin make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Thu Feb 13 11:27:30 EST 2025.

(base) [ehspector@login2 install]$ cd (base) [ehspector@login2 ~]$ home (base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/ (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.out no_gas.in 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out_scored.mol2 no_gas.out gas_2.in gas_4.in gas.in no_gas.out_scored.mol2 gas_2.out gas_4.out gas.out test.mol2 gas_2.out_scored.mol2 gas_4.out_scored.mol2 gas.out_scored.mol2 test_nocharge.mol2 gas_3.in gas_5.in no_charge (base) [ehspector@login2 gas_teiger]$ mkdir test (base) [ehspector@login2 gas_teiger]$ vi gas_3.in (base) [ehspector@login2 gas_teiger]$ mv test_nocharge.mol2 test (base) [ehspector@login2 gas_teiger]$ mv gas_3.in mv: missing destination file operand after ‘gas_3.in’ Try 'mv --help' for more information. (base) [ehspector@login2 gas_teiger]$ mv gas_3.in test (base) [ehspector@login2 gas_teiger]$ cd test/ (base) [ehspector@login2 test]$ ls gas_3.in test_nocharge.mol2 (base) [ehspector@login2 test]$ vi test_nocharge.mol2 (base) [ehspector@login2 test]$ vi gas_3.in (base) [ehspector@login2 test]$ dock6 -i gas_3.in -o gas_3.out (base) [ehspector@login2 test]$ ls gas_3.in gas_3.out gas_3.out_scored.mol2 test_nocharge.mol2 (base) [ehspector@login2 test]$ vi gas_3.out (base) [ehspector@login2 test]$ vi gas_3.out_scored.mol2 (base) [ehspector@login2 test]$ vi gas_3.out (base) [ehspector@login2 test]$ cd .. (base) [ehspector@login2 gas_teiger]$ cd .. (base) [ehspector@login2 4s0v]$ cd gas_teiger/ (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.in gas.out_scored.mol2 test 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out no_charge test.mol2 gas_2.in gas_4.in gas_5.out_scored.mol2 no_gas.in gas_2.out gas_4.out gas.in no_gas.out gas_2.out_scored.mol2 gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_4.in (base) [ehspector@login2 gas_teiger]$ vi gas_4.in (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@login2 gas_teiger]$ ls 1AAQ_noG.mol2 gas_3.out gas_5.in gas.out_scored.mol2 test 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out no_charge test.mol2 gas_2.in gas_4.in gas_5.out_scored.mol2 no_gas.in gas_2.out gas_4.out gas.in no_gas.out gas_2.out_scored.mol2 gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2 (base) [ehspector@login2 gas_teiger]$ cd .. (base) [ehspector@login2 4s0v]$ cd gas_teiger/ (base) [ehspector@login2 gas_teiger]$ mv gas_4.in test (base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2 mv: missing destination file operand after ‘1AAQ_noG.mol2’ Try 'mv --help' for more information. (base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2 test (base) [ehspector@login2 gas_teiger]$ home (base) [ehspector@login2 espector]$ rd srun: error: invalid partition specified: short-40core srun: error: Unable to allocate resources: Invalid partition name specified (base) [ehspector@login2 espector]$ exit logout Connection to login.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ rd srun: job 928167 queued and waiting for resources ^Csrun: Job allocation 928167 has been revoked srun: Force Terminated job 928167 (base) [ehspector@milan1 ~]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       0:23      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:11:38      3 dg[032,035-036]

(base) [ehspector@milan1 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       0:30      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:11:45      3 dg[032,035-036]

(base) [ehspector@milan1 ~]$ cd .. (base) [ehspector@milan1 home]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/1O86/007_virtualscreen/ (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan1 007_virtualscreen]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 1 mix@ a100-02 a100 up 8:00:00 2 alloc@ a100-[07,09] a100 up 8:00:00 1 drain* a100-01 a100 up 8:00:00 2 mix a100-[03,05] a100 up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-large up 8:00:00 1 mix@ a100-02 a100-large up 8:00:00 2 alloc@ a100-[07,09] a100-large up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 2 mix a100-[03,05] a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11] a100-long up 2-00:00:00 1 mix@ a100-02 a100-long up 2-00:00:00 2 alloc@ a100-[07,09] a100-long up 2-00:00:00 1 drain* a100-01 a100-long up 2-00:00:00 2 mix a100-[03,05] a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11] debug-40core up 1:00:00 6 plnd dn[024-025,054,056-058] debug-40core up 1:00:00 5 alloc@ dn[026,029,035,038,045] debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 5 mix dn[004-005,018,051,061] debug-40core up 1:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] extended-40core up 7-00:00:00 6 plnd dn[024-025,054,056-058] extended-40core up 7-00:00:00 5 alloc@ dn[026,029,035,038,045] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 5 mix dn[004-005,018,051,061] extended-40core up 7-00:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] extended-40core-shared up 3-12:00:00 6 plnd dn[024-025,054,056-058] extended-40core-shared up 3-12:00:00 5 alloc@ dn[026,029,035,038,045] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 5 mix dn[004-005,018,051,061] extended-40core-shared up 3-12:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] extended-96core up 7-00:00:00 1 mix@ dg040 extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core up 7-00:00:00 2 mix dg[009,023] extended-96core up 7-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] extended-96core up 7-00:00:00 3 idle dg[042,046-047] extended-96core-shared up 3-12:00:00 1 mix@ dg040 extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] extended-96core-shared up 3-12:00:00 2 mix dg[009,023] extended-96core-shared up 3-12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] extended-96core-shared up 3-12:00:00 3 idle dg[042,046-047] hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047] hbm-1tb-long-96core up 2-00:00:00 1 idle xm048 hbm-extended-96core up 7-00:00:00 3 plnd xm[003,006-007] hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-extended-96core up 7-00:00:00 1 drain xm017 hbm-extended-96core up 7-00:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-large-96core up 8:00:00 3 plnd xm[003,006-007] hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-large-96core up 8:00:00 1 drain xm017 hbm-large-96core up 8:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-long-96core up 2-00:00:00 3 plnd xm[003,006-007] hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-long-96core up 2-00:00:00 1 drain xm017 hbm-long-96core up 2-00:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-medium-96core up 12:00:00 3 plnd xm[003,006-007] hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-medium-96core up 12:00:00 1 drain xm017 hbm-medium-96core up 12:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094] hbm-short-96core up 4:00:00 3 plnd xm[003,006-007] hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051] hbm-short-96core up 4:00:00 1 drain xm017 hbm-short-96core up 4:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094] large-40core up 8:00:00 6 plnd dn[024-025,054,056-058] large-40core up 8:00:00 5 alloc@ dn[026,029,035,038,045] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 5 mix dn[004-005,018,051,061] large-40core up 8:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] large-96core up 8:00:00 1 mix@ dg040 large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043] large-96core up 8:00:00 2 mix dg[009,023] large-96core up 8:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] large-96core up 8:00:00 3 idle dg[042,046-047] long-40core up 2-00:00:00 6 plnd dn[024-025,054,056-058] long-40core up 2-00:00:00 5 alloc@ dn[026,029,035,038,045] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 5 mix dn[004-005,018,051,061] long-40core up 2-00:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] long-40core-shared up 1-00:00:00 6 plnd dn[024-025,054,056-058] long-40core-shared up 1-00:00:00 5 alloc@ dn[026,029,035,038,045] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 5 mix dn[004-005,018,051,061] long-40core-shared up 1-00:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] long-96core up 2-00:00:00 1 mix@ dg040 long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core up 2-00:00:00 2 mix dg[009,023] long-96core up 2-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] long-96core up 2-00:00:00 3 idle dg[042,046-047] long-96core-shared up 1-00:00:00 1 mix@ dg040 long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043] long-96core-shared up 1-00:00:00 2 mix dg[009,023] long-96core-shared up 1-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] long-96core-shared up 1-00:00:00 3 idle dg[042,046-047] medium-40core up 12:00:00 6 plnd dn[024-025,054,056-058] medium-40core up 12:00:00 5 alloc@ dn[026,029,035,038,045] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 5 mix dn[004-005,018,051,061] medium-40core up 12:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] medium-96core up 12:00:00 1 mix@ dg040 medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043] medium-96core up 12:00:00 2 mix dg[009,023] medium-96core up 12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] medium-96core up 12:00:00 3 idle dg[042,046-047] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 6 plnd dn[024-025,054,056-058] short-40core up 4:00:00 5 alloc@ dn[026,029,035,038,045] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 5 mix dn[004-005,018,051,061] short-40core up 4:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] short-40core-shared up 4:00:00 6 plnd dn[024-025,054,056-058] short-40core-shared up 4:00:00 5 alloc@ dn[026,029,035,038,045] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 5 mix dn[004-005,018,051,061] short-40core-shared up 4:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062] short-96core up 4:00:00 1 mix@ dg040 short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core up 4:00:00 2 mix dg[009,023] short-96core up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] short-96core up 4:00:00 3 idle dg[042,046-047] short-96core-shared up 4:00:00 1 mix@ dg040 short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043] short-96core-shared up 4:00:00 2 mix dg[009,023] short-96core-shared up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048] short-96core-shared up 4:00:00 3 idle dg[042,046-047] (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.in (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928174 (base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       3:06      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:14:21      3 dg[032,035-036]

(base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       3:49      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:15:04      3 dg[032,035-036]

(base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       3:52      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:15:07      3 dg[032,035-036]

(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh (base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh Submitted batch job 928179 (base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928179 short-96c 1O86_vs_ ehspecto PD       0:00      3 (Priority)
           928070 short-96c 5een_vs_ ehspecto  R       4:21      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:15:36      3 dg[032,035-036]

(base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928179 short-96c 1O86_vs_ ehspecto PD       0:00      3 (Priority)
           928070 short-96c 5een_vs_ ehspecto  R       4:22      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:15:37      3 dg[032,035-036]

(base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       4:55      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:16:10      3 dg[032,035-036]
           928179 short-96c 1O86_vs_ ehspecto  R       0:24      3 dg[026,046-047]

(base) [ehspector@milan1 007_virtualscreen]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R       5:47      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:17:02      3 dg[032,035-036]
           928179 short-96c 1O86_vs_ ehspecto  R       1:16      3 dg[026,046-047]

(base) [ehspector@milan1 007_virtualscreen]$ home (base) [ehspector@milan1 espector]$ rd srun: job 928192 queued and waiting for resources srun: job 928192 has been allocated resources (base) [ehspector@dn050 espector]$ cd builds/alpha_branch/install/ (base) [ehspector@dn050 install]$ ls bluegenel docker gnu.parallel homebrew intel.intelmpi.parallel Makefile sgi bluegenep gnu gnu.parallel.rdkit homebrew.rdkit intel.ip.mkl oneapi sgi.parallel config.h gnu.acml gnu.rdkit ibmaix intel.mkl pgi test configure gnu.gdb gnu.valgrind intel intel.parallel rules.h (base) [ehspector@dn050 install]$ configure gnu.rdkit bash: configure: command not found (base) [ehspector@dn050 install]$ ./configure gnu.rdkit The requested configuration file was found.

Warning: the configuration file already exists with the creation stamp:

Created at Wed Feb 12 10:29:31 EST 2025 via ./configure gnu

It will be overwritten !

Don't forget to make clean before rebuilding. To reconfigure and rebuild everything start with make -i distclean: Reconfiguring after make -i distclean will avoid this warning.

The DOCK configuration file has been created.

REQUIREMENTS - define these environment variables
RDBASE is the root directory of RDKit
BOOST is the root directory of Boost

(base) [ehspector@dn050 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn050 install]$ make dock Starting installation of DOCK v6.12 program dock at Thu Feb 13 11:55:37 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fingerprint.h:13,
                from fingerprint.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fingerprint.h:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fraggraph.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fraggraph.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fragment.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from gasteiger.h:8,
                from gasteiger.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from gasteiger.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from hungarian.h:7,
                from hungarian.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from hungarian.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from library_file.h:9,
                from library_file.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from library_file.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from limit_max_change.h:12,
                from limit_max_change.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from limit_max_change.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from master_conf.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from master_conf.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from master_score.cpp:2:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from master_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from orient.h:7,
                from orient.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from orient.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from sasa.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from sasa.h:14:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_amber.cpp:66:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_amber.cpp:55:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_chemgrid.cpp:39:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_chemgrid.cpp:38:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_descriptor.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_descriptor.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_footprint.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_footprint.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_ph4.h:7,
                from score_ph4.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_ph4.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_volume.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_volume.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_gist.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_gist.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_hbond.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_hbond.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_internal.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_internal.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_multigrid.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_multigrid.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_sasa.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_sasa.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_solvent.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_solvent.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from simplex.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from simplex.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from utils.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from utils.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.h:12,
                from iso_align.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fragment.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
                from rdtyper.cpp:18:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from rdtyper.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from rddrive.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from dockmol.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

cd nab && make all make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs mv dock6.rdkit ../../bin make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Thu Feb 13 11:58:47 EST 2025.

(base) [ehspector@dn050 install]$ cd .. (base) [ehspector@dn050 alpha_branch]$ exit exit (base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/test/ (base) [ehspector@milan1 test]$ ls 1AAQ_noG.mol2 gas_3.in gas_3.out gas_3.out_scored.mol2 gas_4.in test_nocharge.mol2 (base) [ehspector@milan1 test]$ vi gas_4.in (base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 test]$ ls 1AAQ_noG.mol2 gas_3.in gas_3.out gas_3.out_scored.mol2 gas_4.in gas_4.out test_nocharge.mol2 (base) [ehspector@milan1 test]$ vi gas_4.out (base) [ehspector@milan1 test]$ vi gas_4.in (base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 test]$ ls 1AAQ_noG.mol2 gas_3.out gas_4.in gas_4.out_scored.mol2 gas_3.in gas_3.out_scored.mol2 gas_4.out test_nocharge.mol2 (base) [ehspector@milan1 test]$ vi gas_4.out (base) [ehspector@milan1 test]$ vi gas_4.in (base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan1 test]$ ls 1AAQ_noG.mol2 gas_3.out gas_4.in gas_4.out_scored.mol2 gas_3.in gas_3.out_scored.mol2 gas_4.out test_nocharge.mol2 (base) [ehspector@milan1 test]$ vi gas_4.out (base) [ehspector@milan1 test]$ vi gas_4.out_scored.mol2 (base) [ehspector@milan1 test]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           928060 short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
           928070 short-96c 5een_vs_ ehspecto  R      16:05      3 dg[007-008,041]
           928053 short-96c 2w26_vs_ ehspecto  R    1:27:20      3 dg[032,035-036]
           928179 short-96c 1O86_vs_ ehspecto  R      11:34      3 dg[026,046-047]

(base) [ehspector@milan1 test]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           928174 ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)

(base) [ehspector@milan2 ~]$ scancel 928174 (base) [ehspector@milan2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan2 ~]$ cd AMS_536/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/007_virtual_screen/ (base) [ehspector@milan2 007_virtual_screen]$ ls virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt (base) [ehspector@milan2 007_virtual_screen]$ grep -c "Name" virtual_scored.mol2 97 (base) [ehspector@milan2 007_virtual_screen]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 5EEN/007_virtualscreen/ (base) [ehspector@milan2 007_virtualscreen]$ ls virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt (base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2 97 (base) [ehspector@milan2 007_virtualscreen]$ cd ../../1O86/007_virtualscreen/ (base) [ehspector@milan2 007_virtualscreen]$ ls virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt (base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2 97 (base) [ehspector@milan2 007_virtualscreen]$ cd ../../ (base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/ (base) [ehspector@milan2 006_footprint]$ pwd /gpfs/home/ehspector/AMS_536/Tutorials/2w26/006_footprint (base) [ehspector@milan2 006_footprint]$ cd ../ (base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan2 007_virtual_screen]$ ls virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt (base) [ehspector@milan2 007_virtual_screen]$ cd ../../5EEN/ (base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/ (base) [ehspector@milan2 007_virtualscreen]$ cd ../ (base) [ehspector@milan2 5EEN]$ cd ../ (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ cd 007_virtualscreen/ (base) [ehspector@milan2 007_virtualscreen]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan2 ~]$ cd AMS_536/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ home (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@milan2 dock]$ ls amber_typer.cpp filter.o mem_info.h score_internal.cpp amber_typer.h fingerprint.cpp mem_info.o score_internal.h amber_typer.o fingerprint.h nab score_internal.o base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp base_grid.h fraggraph.cpp nab.h score_multigrid.h base_grid.o fraggraph.h orient.cpp score_multigrid.o base_mpi.cpp fraggraph.o orient.h score.o base_mpi.h fragment.cpp orient.o score_ph4.cpp base_mpi.o fragment.h rddrive.cpp score_ph4.h base_score.cpp fragment.o rddrive.h score_ph4.o base_score.h gasteiger.cpp rddrive.o score_sasa.cpp base_score.o gasteiger.h rdtyper.cpp score_sasa.h conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp conf_gen_ag.o grid.h README score_solvent.h conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o conf_gen_cg.h gzstream sasa.h score_volume.cpp conf_gen_cg.o hungarian.cpp sasa.o score_volume.h conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h conf_gen_ga.cpp library_file.h score.cpp sphere.o conf_gen_ga.h library_file.o score_descriptor.cpp tnt conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl conf_gen_hdb.o lol score_footprint.h trace.o defreal.h Makefile score_footprint.o utils.cpp dock.cpp master_conf.cpp score_gist.cpp utils.h dockmol.cpp master_conf.h score_gist.h utils.o dockmol.h master_conf.o score_gist.o version.h dockmol.o master_score.cpp score.h xlogp.cpp dock.o master_score.h score_hbond.cpp xlogp.h filter.cpp master_score.o score_hbond.h filter.h mem_info.cpp score_hbond.o (base) [ehspector@milan2 dock]$ ls amber_typer.cpp filter.o mem_info.h score_internal.cpp amber_typer.h fingerprint.cpp mem_info.o score_internal.h amber_typer.o fingerprint.h nab score_internal.o base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp base_grid.h fraggraph.cpp nab.h score_multigrid.h base_grid.o fraggraph.h orient.cpp score_multigrid.o base_mpi.cpp fraggraph.o orient.h score.o base_mpi.h fragment.cpp orient.o score_ph4.cpp base_mpi.o fragment.h rddrive.cpp score_ph4.h base_score.cpp fragment.o rddrive.h score_ph4.o base_score.h gasteiger.cpp rddrive.o score_sasa.cpp base_score.o gasteiger.h rdtyper.cpp score_sasa.h conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp conf_gen_ag.o grid.h README score_solvent.h conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o conf_gen_cg.h gzstream sasa.h score_volume.cpp conf_gen_cg.o hungarian.cpp sasa.o score_volume.h conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h conf_gen_ga.cpp library_file.h score.cpp sphere.o conf_gen_ga.h library_file.o score_descriptor.cpp tnt conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl conf_gen_hdb.o lol score_footprint.h trace.o defreal.h Makefile score_footprint.o utils.cpp dock.cpp master_conf.cpp score_gist.cpp utils.h dockmol.cpp master_conf.h score_gist.h utils.o dockmol.h master_conf.o score_gist.o version.h dockmol.o master_score.cpp score.h xlogp.cpp dock.o master_score.h score_hbond.cpp xlogp.h filter.cpp master_score.o score_hbond.h filter.h mem_info.cpp score_hbond.o (base) [ehspector@milan2 dock]$ grep parameters ^C (base) [ehspector@milan2 dock]$ grep -c "parameters" ^C (base) [ehspector@milan2 dock]$ grep -c "parameters" library_file.cpp 3 (base) [ehspector@milan2 dock]$ vi library_file.cpp (base) [ehspector@milan2 dock]$ vi filter.cpp (base) [ehspector@milan2 dock]$ vi filter.cpp (base) [ehspector@milan2 dock]$ vi dockmol.cpp (base) [ehspector@milan2 dock]$ rd srun: job 931653 queued and waiting for resources srun: job 931653 has been allocated resources (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:28:08 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘mol_status’

 917 |     if (filter.mol_status = false){
     |                ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:30:26 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (filter.gasteigerize.mol_status = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ ls alpha_branch dock6-master dock6-master.zip dock6-rdkit (base) [ehspector@dn033 builds]$ cd alpha_branch/src/ (base) [ehspector@dn033 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@dn033 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@dn033 src]$ cd dock (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:33:59 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (filter.gasteigerize.mol_status = no){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

dockmol.cpp:917:42: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?

 917 |     if (filter.gasteigerize.mol_status = no){
     |                                          ^~
     |                                          boost::concepts::detail::no

In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here

  19 |   typedef char (&no)[2];
     |                  ^~

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn033 dock]$ ls amber_typer.cpp conf_gen_hdb.o master_conf.cpp score.h amber_typer.h defreal.h master_conf.h score_hbond.cpp amber_typer.o dock.cpp master_score.cpp score_hbond.h base_grid.cpp dockmol.cpp master_score.h score_internal.cpp base_grid.h dockmol.h mem_info.cpp score_internal.h base_grid.o dock.o mem_info.h score_multigrid.cpp base_mpi.cpp filter.cpp nab score_multigrid.h base_mpi.h filter.h nabcode.h score_ph4.cpp base_mpi.o fingerprint.cpp nab.h score_ph4.h base_score.cpp fingerprint.h orient.cpp score_sasa.cpp base_score.h fraggraph.cpp orient.h score_sasa.h base_score.o fraggraph.h rddrive.cpp score_solvent.cpp conf_gen_ag.cpp fragment.cpp rddrive.h score_solvent.h conf_gen_ag.h fragment.h rdtyper.cpp score_volume.cpp conf_gen_ag.o gasteiger.cpp rdtyper.h score_volume.h conf_gen_cg.cpp gasteiger.h README simplex.cpp conf_gen_cg.h grid.cpp sasa.cpp simplex.h conf_gen_cg.o grid.h sasa.h sphere.cpp conf_gen_dn.cpp gzstream score_amber.cpp sphere.h conf_gen_dn_ga.cpp hungarian.cpp score_amber.h tnt conf_gen_dn_ga.h hungarian.h score_chemgrid.cpp trace.cpp conf_gen_dn_ga.o iso_align.cpp score_chemgrid.h trace.h conf_gen_dn.h iso_align.h score.cpp trace.inl conf_gen_dn.o library_file.cpp score_descriptor.cpp utils.cpp conf_gen_ga.cpp library_file.h score_descriptor.h utils.h conf_gen_ga.h limit_max_change.cpp score_footprint.cpp version.h conf_gen_ga.o limit_max_change.h score_footprint.h xlogp.cpp conf_gen_hdb.cpp lol score_gist.cpp xlogp.h conf_gen_hdb.h Makefile score_gist.h (base) [ehspector@dn033 dock]$ vi filter.cpp (base) [ehspector@dn033 dock]$ vi filter.h (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../ (base) [ehspector@dn033 alpha_branch]$ ls bin docs parameters README.md template_pipeline developer install README src tutorials (base) [ehspector@dn033 alpha_branch]$ cd src/ (base) [ehspector@dn033 src]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:45:39 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (filter.gasteigerize.mol_status = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd src/ (base) [ehspector@dn033 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@dn033 src]$ cd dock (base) [ehspector@dn033 dock]$ vi filter.cpp (base) [ehspector@dn033 dock]$ cd ../ (base) [ehspector@dn033 src]$ vi dockmol.cpp (base) [ehspector@dn033 src]$ cd dock (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:52:20 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (filter.gasteigerize.mol_status = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd .. (base) [ehspector@dn033 alpha_branch]$ cd src/dock (base) [ehspector@dn033 dock]$ vi filter.cpp (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd .. (base) [ehspector@dn033 src]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ ls bluegenel gnu.acml homebrew intel.mkl sgi bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel config.h gnu.parallel ibmaix Makefile test configure gnu.parallel.rdkit intel oneapi docker gnu.rdkit intel.intelmpi.parallel pgi gnu gnu.valgrind intel.ip.mkl rules.h (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:55:45 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp dockmol.cpp:917:43: warning: multi-character character constant [-Wmultichar]

 917 |     if (filter.gasteigerize.mol_status == 'no'){
     |                                           ^Stonybrook (talk)

In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (filter.gasteigerize.mol_status == 'no'){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd .. (base) [ehspector@dn033 alpha_branch]$ cd src/dock (base) [ehspector@dn033 dock]$ vi filter.cpp (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 16:58:13 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (filter.gasteigerize.mol_status = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn033 dock]$ vi library_file.cpp (base) [ehspector@dn033 dock]$ vi library_file.h (base) [ehspector@dn033 dock]$ vi filter.cpp (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 17:06:34 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:29: error: ‘mol_status’ was not declared in this scope

 917 |     if (filter.gasteigerize(mol_status) = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

dockmol.cpp:917:39: error: expression cannot be used as a function

 917 |     if (filter.gasteigerize(mol_status) = false){
     |                                       ^

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ vi filter.cpp (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn033 dock]$ vi filter.cpp (base) [ehspector@dn033 dock]$ vi filter.h (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd .. (base) [ehspector@dn033 src]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 17:16:17 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:917:30: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 917 |     if (!filter.gasteigerize.mol_status){
     |                              ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd src/dock (base) [ehspector@dn033 dock]$ vi library_file.cpp (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 17:59:26 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:780:5: error: ‘mol_status’ was not declared in this scope

 780 |     mol_status = false;
     |     ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 919 |     if (filter.gasteigerize.mol_status){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ vi dockmol.cpp (base) [ehspector@dn033 install]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd ../ (base) [ehspector@dn033 builds]$ cd ../ (base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd .. (base) [ehspector@dn033 src]$ cd ../ (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 18:02:33 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 919 |     if (filter.gasteigerize.mol_status = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd alpha_branch/src/ (base) [ehspector@dn033 src]$ ;s bash: syntax error near unexpected token `;' (base) [ehspector@dn033 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@dn033 src]$ cd dock (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 18:06:37 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:919:16: error: ‘gasteigerize’ is not a class, namespace, or enumeration

 919 |     if (filter.gasteigerize::mol_status = no){
     |                ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~

dockmol.cpp:919:43: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?

 919 |     if (filter.gasteigerize::mol_status = no){
     |                                           ^~
     |                                           boost::concepts::detail::no

In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here

  19 |   typedef char (&no)[2];
     |                  ^~

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ vi dockmol.cpp (base) [ehspector@dn033 install]$ cd .. (base) [ehspector@dn033 alpha_branch]$ cd install/ (base) [ehspector@dn033 install]$ ls bluegenel gnu.acml homebrew intel.mkl sgi bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel config.h gnu.parallel ibmaix Makefile test configure gnu.parallel.rdkit intel oneapi docker gnu.rdkit intel.intelmpi.parallel pgi gnu gnu.valgrind intel.ip.mkl rules.h (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd .. (base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 18:11:54 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:919:16: error: ‘class Filter’ has no member named ‘mol_status’

 919 |     if (filter.mol_status = false){
     |                ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd .. (base) [ehspector@dn033 alpha_branch]$ cd .. (base) [ehspector@dn033 builds]$ cd alpha_branch/src/ (base) [ehspector@dn033 src]$ ;s bash: syntax error near unexpected token `;' (base) [ehspector@dn033 src]$ ls accessories dock gbsa_grids Makefile rdkit tleap antechamber docktools grid mopac6 resp (base) [ehspector@dn033 src]$ cd dock (base) [ehspector@dn033 dock]$ ls amber_typer.cpp conf_gen_hdb.o master_conf.cpp score.h amber_typer.h defreal.h master_conf.h score_hbond.cpp amber_typer.o dock.cpp master_score.cpp score_hbond.h base_grid.cpp dockmol.cpp master_score.h score_internal.cpp base_grid.h dockmol.h mem_info.cpp score_internal.h base_grid.o dock.o mem_info.h score_multigrid.cpp base_mpi.cpp filter.cpp nab score_multigrid.h base_mpi.h filter.h nabcode.h score_ph4.cpp base_mpi.o fingerprint.cpp nab.h score_ph4.h base_score.cpp fingerprint.h orient.cpp score_sasa.cpp base_score.h fraggraph.cpp orient.h score_sasa.h base_score.o fraggraph.h rddrive.cpp score_solvent.cpp conf_gen_ag.cpp fragment.cpp rddrive.h score_solvent.h conf_gen_ag.h fragment.h rdtyper.cpp score_volume.cpp conf_gen_ag.o gasteiger.cpp rdtyper.h score_volume.h conf_gen_cg.cpp gasteiger.h README simplex.cpp conf_gen_cg.h grid.cpp sasa.cpp simplex.h conf_gen_cg.o grid.h sasa.h sphere.cpp conf_gen_dn.cpp gzstream score_amber.cpp sphere.h conf_gen_dn_ga.cpp hungarian.cpp score_amber.h tnt conf_gen_dn_ga.h hungarian.h score_chemgrid.cpp trace.cpp conf_gen_dn_ga.o iso_align.cpp score_chemgrid.h trace.h conf_gen_dn.h iso_align.h score.cpp trace.inl conf_gen_dn.o library_file.cpp score_descriptor.cpp utils.cpp conf_gen_ga.cpp library_file.h score_descriptor.h utils.h conf_gen_ga.h limit_max_change.cpp score_footprint.cpp version.h conf_gen_ga.o limit_max_change.h score_footprint.h xlogp.cpp conf_gen_hdb.cpp lol score_gist.cpp xlogp.h conf_gen_hdb.h Makefile score_gist.h (base) [ehspector@dn033 dock]$ vi dockmol.cpp (base) [ehspector@dn033 dock]$ cd ../../install/ (base) [ehspector@dn033 install]$ make dock Starting installation of DOCK v6.12 program dock at Sun Feb 16 18:14:22 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp makIn file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’: dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’

 919 |     if (filter.gasteigerize.mol_status = false){
     |                             ^12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn033 install]$ cd ../../ (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn033 dock]$ vi filter.h (base) [ehspector@dn033 dock]$ exit exit (base) [ehspector@milan2 dock]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Permission denied, please try again. ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ home (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock (base) [ehspector@milan2 dock]$ vi filter.cpp (base) [ehspector@milan2 dock]$ vi filter.cpp (base) [ehspector@milan2 dock]$ vi dockmol.cpp (base) [ehspector@milan2 dock]$ rd srun: job 932106 queued and waiting for resources srun: job 932106 has been allocated resources (base) [ehspector@dn035 dock]$ cd ../../install/ (base) [ehspector@dn035 install]$ ls bluegenel gnu.acml homebrew intel.mkl sgi bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel config.h gnu.parallel ibmaix Makefile test configure gnu.parallel.rdkit intel oneapi docker gnu.rdkit intel.intelmpi.parallel pgi gnu gnu.valgrind intel.ip.mkl rules.h (base) [ehspector@dn035 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn035 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 10:08:08 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

filter.cpp:214:7: error: expected unqualified-id before ‘else’

 214 |     } else {
     |       ^Stonybrook (talk)

filter.cpp:221:5: error: ‘message’ does not name a type

 221 |     message = get_descriptors(mol);
     |     ^12:36, 21 February 2025 (EST)~

filter.cpp:222:5: error: ‘cout’ does not name a type

 222 |     cout << message << endl;
     |     ^Stonybrook (talk)

filter.cpp:223:1: error: expected declaration before ‘}’ token

 223 | }
     | ^

make[1]: *** [../../install/rules.h:36: filter.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn035 install]$ module load git (base) [ehspector@dn035 install]$ git diff diff --git a/docs/new_in_6.13.txt b/docs/new_in_6.13.txt index 7b10f318..fac269c6 100644 --- a/docs/new_in_6.13.txt +++ b/docs/new_in_6.13.txt @@ -29,6 +29,14 @@ Ligand Efficiency added for Descriptor Score

    Users can now toggle ligand efficiency on/off when using grid_score in descriptor score.
    Ligand efficiency can be used alongside with grid score and will be calculated as the grid score divided by the number of heavy atoms.

+Gasterization of molecules in database filter + Users can now apply gasteiger charges using the databasefilter question tree + instead of having to gasterize molecules through the GA. This will be a useful + tool in benchmarking dock as well as understanding the electrostatics of a + protein environment. + Disclaimer: gasterization can be used as long as the molecule is precharged + and acts mainly as an interconversion function. +

Miscellaneous

Mutation Selection algorithmic changes for DOCK_GA

@@ -36,6 +44,8 @@ Mutation Selection algorithmic changes for DOCK_GA

    the GA will not select a mutation type and then select a fragment
    incompatible with the selected mutation type.

+If users use sphere files, DOCK6 will print out the number of spheres used. +

12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

BUG FIXES

@@ -67,6 +77,8 @@ definitions added:

 definition    N.am
 ______________________________________________________________________

+Pertaining to the RDKit compilation with DOCK6, previous versions of DOCK6 included +a broken Boost url for download. Hence, we have replaced it with a working url.

12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

@@ -88,6 +100,8 @@ For DOCK_GA:

    ga_constraint_lower_mol_wt          [0]
    ga_constraint_lower_mol_wt          [0]
    ga_constraint_mol_wt_std_dev        [35.0]

+For Database Filter: + dbfilter_gasteiger_charges [no] (yes no)

12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

@@ -111,6 +125,10 @@ KNOWN BUGS

    3. In the flex.defn file, there is a flag minimize which is disabled.
       (The flag has no impact on the calculation.) All torsions are 
       Minimized.

+ + 4. Gasterization can be used as long as the molecule is precharged + and acts mainly as an interconversion function.Additionally,ions + will give calculating difficulty.

12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

diff --git a/src/dock/dockmol.cpp b/src/dock/dockmol.cpp index 34811840..2f964a80 100644 --- a/src/dock/dockmol.cpp +++ b/src/dock/dockmol.cpp @@ -35,7 +35,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

#include <iomanip> 
#include <string.h>
#include "dockmol.h"

- +#include "filter.h"

#ifdef BUILD_DOCK_WITH_RDKIT
#include <fstream>
// RDKit stuff

@@ -539,14 +539,14 @@ Read_Mol2_retain(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvat

            mol.subst_names[i] = subst_name;//mol.title
        }
    }

- // If all partial charges are zero, it is a bad molecule + //If all partial charges are zero, it is a bad molecule

    int num_zeros = 0;
    for (int i = 0; i < mol.num_atoms; ++i){
        if (mol.charges[i] == 0.0){
            num_zeros += 1;
        }
    }

- // Is it a bad molecule? + //Is it a bad molecule?

    if (num_zeros == mol.num_atoms){
        mol.bad_molecule = true;
    }

- // Is it a bad molecule? + //Is it a bad molecule?

    if (num_zeros == mol.num_atoms){
        mol.bad_molecule = true;
    } else {

@@ -775,7 +775,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,

    bool            check_cols = false;
    bool            seven_columns = false; // default @<TRIPOS>ATOM line has 9 columns. By GDRM
    //int             bad_line{0}; // number of bad atom lines. By GDRM

- + //declaring classes for gasteiger bypass EHS 2/16/25 + Filter filter; + Filter mol_status;

    // init state vars
    atom_line = false;

@@ -913,6 +915,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,

        }
    }
    // If all partial charges are zero, it is a bad molecule

+ // Skip over if gasterizing a molecule with no charges EHS 2/13/25 + if (filter.gasteigerize){ + goto skip;

    int num_zeros = 0;
    for (int i = 0; i < mol.num_atoms; ++i){
        if (mol.charges[i] == 0.0){

@@ -925,6 +930,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,

    } else {
        mol.bad_molecule = false;
    }

+} + skip: + cout << "This Molecule has no charges and will be gasterized" << endl;

    // skip down to the bond section
    for (;;) {

diff --git a/src/dock/filter.cpp b/src/dock/filter.cpp index b8469418..58f9c742 100644 --- a/src/dock/filter.cpp +++ b/src/dock/filter.cpp @@ -196,14 +196,14 @@ void Filter::calc_descriptors(DOCKMol & mol, AMBER_TYPER & c_typer)

        }

        // placing a gasteiger flag this will be similar to ga code

- if ( gasteigerize ){ - //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25 - activate_mol(mol); + if ( gasteigerize && mol.bad_molecule == false ){ + //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25 + activate_mol(mol); (base) [ehspector@dn035 install]$ (base) [ehspector@dn035 install]$ exit exit (base) [ehspector@milan2 dock]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ home (base) [ehspector@milan2 espector]$ cd 4s0v/ (base) [ehspector@milan2 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@milan2 4s0v]$ cd gas_teiger/ (base) [ehspector@milan2 gas_teiger]$ ls 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out_scored.mol2 no_gas.in gas_2.in gas_4.out gas.in no_gas.out gas_2.out gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2 gas_2.out_scored.mol2 gas_5.in gas.out_scored.mol2 test gas_3.out gas_5.out no_charge test.mol2 (base) [ehspector@milan2 gas_teiger]$ cd test/ (base) [ehspector@milan2 test]$ ls 1AAQ_noG.mol2 gas_3.out gas_4.in gas_4.out_scored.mol2 gas_3.in gas_3.out_scored.mol2 gas_4.out test_nocharge.mol2 (base) [ehspector@milan2 test]$ vi gas_4.out (base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2 (base) [ehspector@milan2 test]$ dock6 -i gas_4.in -o gas_4.out (base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2 (base) [ehspector@milan2 test]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ home (base) [ehspector@milan1 espector]$ cd 4s0v/ (base) [ehspector@milan1 4s0v]$ ls cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres Denovodata flex_docking fragLib gridbox virtual_screening deNovorefinement flex_docking_mpi GA reScore dock6_v_dock6mpi focusGrowth GA_data rigid_docking energy_min focusReScore gas_teiger structure (base) [ehspector@milan1 4s0v]$ cd ../builds/alpha_branch/src/ (base) [ehspector@milan1 src]$ cd dock (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ vi dock.cpp (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ grep -wc Read_Mol2 * amber_typer.cpp:0 amber_typer.h:0 amber_typer.o:0 base_grid.cpp:0 base_grid.h:0 base_grid.o:0 base_mpi.cpp:0 base_mpi.h:0 base_mpi.o:0 base_score.cpp:0 base_score.h:0 base_score.o:0 conf_gen_ag.cpp:0 conf_gen_ag.h:0 conf_gen_ag.o:0 conf_gen_cg.cpp:0 conf_gen_cg.h:0 conf_gen_cg.o:0 conf_gen_dn.cpp:2 conf_gen_dn_ga.cpp:1 conf_gen_dn_ga.h:0 conf_gen_dn_ga.o:0 conf_gen_dn.h:0 conf_gen_dn.o:0 conf_gen_ga.cpp:1 conf_gen_ga.h:0 conf_gen_ga.o:0 conf_gen_hdb.cpp:0 conf_gen_hdb.h:0 conf_gen_hdb.o:0 defreal.h:0 dock.cpp:0 dockmol.cpp:1 dockmol.h:1 dockmol.o:0 dock.o:0 filter.cpp:0 filter.h:0 fingerprint.cpp:1 fingerprint.h:0 fraggraph.cpp:0 fraggraph.h:0 fragment.cpp:0 fragment.h:0 gasteiger.cpp:0 gasteiger.h:0 grid.cpp:0 grid.h:0 grep: gzstream: Is a directory gzstream:0 hungarian.cpp:0 hungarian.h:0 iso_align.cpp:0 iso_align.h:0 library_file.cpp:2 library_file.h:0 limit_max_change.cpp:0 limit_max_change.h:0 lol:0 Makefile:0 master_conf.cpp:0 master_conf.h:0 master_score.cpp:0 master_score.h:0 mem_info.cpp:0 mem_info.h:0 grep: nab: Is a directory nab:0 nabcode.h:0 nab.h:0 orient.cpp:0 orient.h:0 rddrive.cpp:0 rddrive.h:0 rdtyper.cpp:0 rdtyper.h:0 README:0 sasa.cpp:0 sasa.h:0 score_amber.cpp:0 score_amber.h:0 score_chemgrid.cpp:0 score_chemgrid.h:0 score.cpp:1 score_descriptor.cpp:2 score_descriptor.h:0 score_footprint.cpp:2 score_footprint.h:0 score_gist.cpp:0 score_gist.h:0 score.h:0 score_hbond.cpp:1 score_hbond.h:0 score_internal.cpp:0 score_internal.h:0 score_multigrid.cpp:1 score_multigrid.h:0 score_ph4.cpp:2 score_ph4.h:0 score_sasa.cpp:1 score_sasa.h:0 score_solvent.cpp:1 score_solvent.h:0 score_volume.cpp:1 score_volume.h:0 simplex.cpp:0 simplex.h:0 sphere.cpp:0 sphere.h:0 grep: tnt: Is a directory tnt:0 trace.cpp:0 trace.h:0 trace.inl:0 utils.cpp:0 utils.h:0 version.h:0 xlogp.cpp:0 xlogp.h:0 (base) [ehspector@milan1 dock]$ vi library_file.cpp (base) [ehspector@milan1 dock]$ vi dock.cpp (base) [ehspector@milan1 dock]$ vi dock.cpp (base) [ehspector@milan1 dock]$ vi dock.cpp (base) [ehspector@milan1 dock]$ vi library_file.cpp (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ vi dock.cpp (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi dock.cpp (base) [ehspector@milan1 dock]$ vi library_file.cpp (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi filter.h (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi filter.h (base) [ehspector@milan1 dock]$ vi filter.cpp (base) [ehspector@milan1 dock]$ vi dockmol.cpp (base) [ehspector@milan1 dock]$ rd srun: job 932383 queued and waiting for resources srun: job 932383 has been allocated resources (base) [ehspector@dn051 dock]$ cd ../../install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 12:54:43 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

filter.cpp:214:7: error: expected unqualified-id before ‘else’

 214 |     } else {
     |       ^Stonybrook (talk)

filter.cpp:221:5: error: ‘message’ does not name a type

 221 |     message = get_descriptors(mol);
     |     ^12:36, 21 February 2025 (EST)~

filter.cpp:222:5: error: ‘cout’ does not name a type

 222 |     cout << message << endl;
     |     ^Stonybrook (talk)

filter.cpp:223:1: error: expected declaration before ‘}’ token

 223 | }
     | ^

make[1]: *** [../../install/rules.h:36: filter.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn051 install]$ cd ../../ (base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn051 dock]$ vi filter.cpp (base) [ehspector@dn051 dock]$ cd ../../install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 13:00:19 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

filter.cpp: In member function ‘void Filter::calc_descriptors(DOCKMol&, AMBER_TYPER&)’: filter.cpp:279:26: error: qualified-id in declaration before ‘(’ token

 279 | bool Filter::fails_filter(DOCKMol & mol)
     |                          ^

filter.cpp:529:31: error: qualified-id in declaration before ‘(’ token

 529 | string Filter::get_descriptors(DOCKMol & mol)
     |                               ^

filter.cpp:591:21: error: qualified-id in declaration before ‘(’ token

 591 | Filter::activate_mol( DOCKMol & mol )
     |                     ^

filter.cpp:605:2: error: expected ‘}’ at end of input

 605 | } // end Filter::activate_mol()
     |  ^

filter.cpp:147:1: note: to match this ‘{’

 147 | {
     | ^

make[1]: *** [../../install/rules.h:36: filter.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn051 install]$ cd ../../alpha_branch/src/dock (base) [ehspector@dn051 dock]$ vi filter.cpp (base) [ehspector@dn051 dock]$ vi filter.cpp (base) [ehspector@dn051 dock]$ cd ../../install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 13:05:08 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fingerprint.h:13,
                from fingerprint.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fingerprint.h:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fraggraph.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fraggraph.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fragment.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from gasteiger.h:8,
                from gasteiger.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from gasteiger.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from hungarian.h:7,
                from hungarian.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from hungarian.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from library_file.h:9,
                from library_file.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from library_file.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from limit_max_change.h:12,
                from limit_max_change.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from limit_max_change.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from master_conf.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from master_conf.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from master_score.cpp:2:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from master_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from orient.h:7,
                from orient.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from orient.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from sasa.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from sasa.h:14:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_amber.cpp:66:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_amber.cpp:55:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_chemgrid.cpp:39:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_chemgrid.cpp:38:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_descriptor.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_descriptor.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_footprint.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_footprint.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_ph4.h:7,
                from score_ph4.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_ph4.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_volume.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_volume.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_gist.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_gist.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_hbond.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_hbond.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_internal.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_internal.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_multigrid.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_multigrid.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_sasa.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_sasa.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_solvent.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_solvent.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from simplex.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from simplex.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from utils.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from utils.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.h:12,
                from iso_align.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fragment.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
                from rdtyper.cpp:18:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from rdtyper.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from rddrive.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from dockmol.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

cd nab && make all make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs mv dock6.rdkit ../../bin make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'

Installation of DOCK v6.12 program dock is complete at Mon Feb 17 13:08:09 EST 2025.

(base) [ehspector@dn051 install]$ cd ../al bash: cd: ../al: No such file or directory (base) [ehspector@dn051 install]$ cd ../../alpha_branch/ (base) [ehspector@dn051 alpha_branch]$ cd src/dock (base) [ehspector@dn051 dock]$ vi filter.cpp (base) [ehspector@dn051 dock]$ vi filter.cpp (base) [ehspector@dn051 dock]$ vi dock.cpp (base) [ehspector@dn051 dock]$ vi library_file.cpp (base) [ehspector@dn051 dock]$ vi dockmol.cpp (base) [ehspector@dn051 dock]$ vi dockmol.cpp (base) [ehspector@dn051 dock]$ cd ../../ (base) [ehspector@dn051 alpha_branch]$ cd install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 13:31:34 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dock.cpp: In function ‘int main(int, char**)’: dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’

 785 |     while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
     |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

In file included from dock.cpp:62: library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’

 141 |     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
     |                     ^12:36, 21 February 2025 (EST)~

library_file.h:141:21: note: candidate expects 7 arguments, 8 provided make[1]: *** [../../install/rules.h:36: dock.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn051 install]$ cd ../ (base) [ehspector@dn051 alpha_branch]$ cd ../ (base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn051 dock]$ vi dock.cpp (base) [ehspector@dn051 dock]$ vi library_file.cpp (base) [ehspector@dn051 dock]$ vi dockmol.cpp (base) [ehspector@dn051 dock]$ ls amber_typer.cpp conf_gen_dn.o gzstream rddrive.h score_multigrid.h amber_typer.h conf_gen_ga.cpp hungarian.cpp rdtyper.cpp score_ph4.cpp amber_typer.o conf_gen_ga.h hungarian.h rdtyper.h score_ph4.h base_grid.cpp conf_gen_ga.o iso_align.cpp README score_sasa.cpp base_grid.h conf_gen_hdb.cpp iso_align.h sasa.cpp score_sasa.h base_grid.o conf_gen_hdb.h library_file.cpp sasa.h score_solvent.cpp base_mpi.cpp conf_gen_hdb.o library_file.h score_amber.cpp score_solvent.h base_mpi.h defreal.h limit_max_change.cpp score_amber.h score_volume.cpp base_mpi.o dock.cpp limit_max_change.h score_chemgrid.cpp score_volume.h base_score.cpp dockmol.cpp lol score_chemgrid.h simplex.cpp base_score.h dockmol.h Makefile score.cpp simplex.h base_score.o filter.cpp master_conf.cpp score_descriptor.cpp sphere.cpp conf_gen_ag.cpp filter.h master_conf.h score_descriptor.h sphere.h conf_gen_ag.h fingerprint.cpp master_score.cpp score_footprint.cpp tnt conf_gen_ag.o fingerprint.h master_score.h score_footprint.h trace.cpp conf_gen_cg.cpp fraggraph.cpp mem_info.cpp score_gist.cpp trace.h conf_gen_cg.h fraggraph.h mem_info.h score_gist.h trace.inl conf_gen_cg.o fragment.cpp nab score.h utils.cpp conf_gen_dn.cpp fragment.h nabcode.h score_hbond.cpp utils.h conf_gen_dn_ga.cpp gasteiger.cpp nab.h score_hbond.h version.h conf_gen_dn_ga.h gasteiger.h orient.cpp score_internal.cpp xlogp.cpp conf_gen_dn_ga.o grid.cpp orient.h score_internal.h xlogp.h conf_gen_dn.h grid.h rddrive.cpp score_multigrid.cpp (base) [ehspector@dn051 dock]$ vi dockmol.cpp (base) [ehspector@dn051 dock]$ vi dock.cpp (base) [ehspector@dn051 dock]$ vi library_file.cpp (base) [ehspector@dn051 dock]$ vi dock.cpp (base) [ehspector@dn051 dock]$ cd ../../ (base) [ehspector@dn051 alpha_branch]$ cd install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 13:40:15 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

dock.cpp: In function ‘int main(int, char**)’: dock.cpp:340:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool, bool, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’

 340 |     while (c_library.get_mol(mol, false, false, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
     |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)

In file included from dock.cpp:62: library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’

 141 |     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
     |                     ^12:36, 21 February 2025 (EST)~

library_file.h:141:21: note: candidate expects 7 arguments, 8 provided dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’

 785 |     while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
     |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk) 12:36, 21 February 2025 (EST)

library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’

 141 |     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
     |                     ^12:36, 21 February 2025 (EST)~

library_file.h:141:21: note: candidate expects 7 arguments, 8 provided make[1]: *** [../../install/rules.h:36: dock.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn051 install]$ cd .. (base) [ehspector@dn051 alpha_branch]$ cd .. (base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock (base) [ehspector@dn051 dock]$ vi library_file.h (base) [ehspector@dn051 dock]$ cd ../../install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 13:45:32 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fingerprint.h:13,
                from fingerprint.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fingerprint.h:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fraggraph.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fraggraph.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fragment.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from gasteiger.h:8,
                from gasteiger.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from gasteiger.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from hungarian.h:7,
                from hungarian.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from hungarian.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from library_file.h:9,
                from library_file.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from library_file.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

library_file.cpp: In member function ‘void Library_File::open_files()’: library_file.cpp:1384:21: error: no matching function for call to ‘Library_File::read_mol(DOCKMol&, bool’

1384 |         if (read_mol(tmp_mol, false))
     |             12:36, 21 February 2025 (EST)Stonybrook (talk)^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)

library_file.h:139:21: note: candidate: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’

 139 |     bool            read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
     |                     ^12:36, 21 February 2025 (EST)~~

library_file.h:139:21: note: candidate expects 3 arguments, 2 provided library_file.cpp: At global scope: library_file.cpp:1435:1: error: no declaration matches ‘bool Library_File::read_mol(DOCKMol&, bool)’

1435 | Library_File::read_mol(DOCKMol & mol, bool read_amber)
     | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~

library_file.h:139:21: note: candidate is: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’

 139 |     bool            read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
     |                     ^12:36, 21 February 2025 (EST)~~

library_file.h:19:17: note: ‘class Library_File’ defined here

  19 | class           Library_File:public Base_MPI {
     |                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~

make[1]: *** [../../install/rules.h:36: library_file.o] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn051 install]$ cd .. (base) [ehspector@dn051 alpha_branch]$ cd src/dock (base) [ehspector@dn051 dock]$ vi dock.cpp (base) [ehspector@dn051 dock]$ vi library_file.cpp (base) [ehspector@dn051 dock]$ cd ../../install/ (base) [ehspector@dn051 install]$ make clean make -C ../src clean make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' make -C dock clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o cd nab && make clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' /bin/rm -f *.o nab.a lex.mm_options.c make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make cleanall make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' /bin/rm -f *.o libgzstream.a test_gzip test_gunzip make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make -C accessories clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' /bin/rm -f showbox.o showsphere.o sphgen.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories' make -C gbsa_grids clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C schemgrid_GB clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB' make -C schemgrid_SA clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids' make -C grid clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid' make -C tleap clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap' make -C antechamber clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' /bin/rm -f *.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber' make -C mopac6/src clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src' make -C resp clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' /bin/rm -f amopen.o lapack.o mexit.o resp.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp' make -C docktools clean make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make -C chemgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids' make -C solvgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids' make -C solvgrids_sev clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' /bin/rm -f sas.o cube.o memalloc.o solvmap.o make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev' make -C convgrids clean make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridconv.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make -f gridrdsl.mk clean make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids' make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools' make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src' (base) [ehspector@dn051 install]$ make dock Starting installation of DOCK v6.12 program dock at Mon Feb 17 13:53:32 EST 2025.

make -C ../src/dock install make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from amber_typer.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from amber_typer.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_mpi.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
                from base_mpi.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from base_score.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from base_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ag.h:5,
                from conf_gen_ag.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ag.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_cg.h:5,
                from conf_gen_cg.cpp:17:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_cg.cpp:8:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn.h:12,
                from conf_gen_dn.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_dn_ga.h:12,
                from conf_gen_dn_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_dn_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_ga.h:13,
                from conf_gen_ga.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from conf_gen_ga.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from conf_gen_hdb.h:4,
                from conf_gen_hdb.cpp:14:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from conf_gen_hdb.cpp:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from dock.cpp:61:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dock.cpp:53:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from dockmol.cpp:37:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from dockmol.cpp:33:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from filter.h:10,
                from filter.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from filter.h:4:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fingerprint.h:13,
                from fingerprint.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fingerprint.h:6:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fraggraph.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fraggraph.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.cpp:3:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from fragment.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from gasteiger.h:8,
                from gasteiger.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from gasteiger.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from hungarian.h:7,
                from hungarian.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from hungarian.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from library_file.h:9,
                from library_file.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from library_file.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from limit_max_change.h:12,
                from limit_max_change.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from limit_max_change.h:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from master_conf.h:6,
                from master_conf.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from master_conf.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from master_score.cpp:2:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from master_score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from orient.h:7,
                from orient.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from orient.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from sasa.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from sasa.h:14:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_amber.cpp:66:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_amber.cpp:55:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_chemgrid.cpp:39:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
                from score_chemgrid.cpp:38:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_descriptor.cpp:10:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_descriptor.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_footprint.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_footprint.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_ph4.h:7,
                from score_ph4.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_ph4.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_volume.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_volume.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_gist.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_gist.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_hbond.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_hbond.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_internal.cpp:8:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_internal.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score_multigrid.cpp:9:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_multigrid.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_sasa.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_sasa.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from score_solvent.h:9,
                from sasa.h:15,
                from score_solvent.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from score_solvent.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from score.h:7,
                from master_score.h:5,
                from simplex.cpp:4:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from simplex.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from utils.cpp:7:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from utils.cpp:1:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from fragment.h:12,
                from iso_align.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
                from fragment.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
                from rdtyper.cpp:18:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
                from rdtyper.cpp:2:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,

                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
                from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
                from dockmol.h:16,
                from rddrive.cpp:1:

/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]

 130 |         struct hash_base : std::unary_function<T, std::size_t> {};
     |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,

                from dockmol.h:5:

/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here

 117 |     struct unary_function
     |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)Stonybrook (talk)

cd nab && make all make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' gcc -c -O3 -D_ANSI_SOURCE molio.c gcc -c -O2 -o prm.o prm.c make is_LEX_available make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c gcc -c -O2 -o traceback.o traceback.c gcc -c -O2 -o select_atoms.o select_atoms.c gcc -c -O2 -o memutil.o memutil.c gcc -c -O2 -o reslib.o reslib.c gcc -c -O2 -o jacobi.o jacobi.c gcc -c -O2 -o molutil.o molutil.c gcc -c -O2 -o chirvol.o chirvol.c gcc -c -O2 -o regexp.o regexp.c gcc -c -O2 -o binpos.o binpos.c gcc -c -O2 -o time.o time.c gcc -c -O3 -D_ANSI_SOURCE rand2.c gcc -c -O3 -D_ANSI_SOURCE conjgrad.c gcc -c -O2 -o database.o database.c gcc -c -O2 -o tleap.o tleap.c ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o ar: creating nab.a a - molio.o a - prm.o a - sff.o a - traceback.o a - select_atoms.o a - memutil.o a - reslib.o a - jacobi.o a - molutil.o a - chirvol.o a - regexp.o a - binpos.o a - time.o a - rand2.o a - conjgrad.o a - database.o a - tleap.o ranlib nab.a make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab' cd gzstream && make make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C ar cr libgzstream.a gzstream.o make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream' g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \ -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs conf_gen_dn.o: In function `DN_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': conf_gen_dn.cpp:(.text+0x1ec40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' conf_gen_dn.o: In function `DN_Build::read_library_anchor(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': conf_gen_dn.cpp:(.text+0x1f508): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' conf_gen_dn_ga.o: In function `DN_GA_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': conf_gen_dn_ga.cpp:(.text+0xdf40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' conf_gen_ga.o: In function `GA_Recomb::read_library(std::vector<DOCKMol, std::allocator<DOCKMol> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': conf_gen_ga.cpp:(.text+0x1d5c5): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' fingerprint.o: In function `Fingerprint::input_parameters(Parameter_Reader&)': fingerprint.cpp:(.text+0x2f14): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' library_file.o:library_file.cpp:(.text+0x6c75): more undefined references to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' follow collect2: error: ld returned 1 exit status make[1]: *** [Makefile:39: dock6.rdkit] Error 1 make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock' make: *** [Makefile:28: dock] Error 2 (base) [ehspector@dn051 install]$ exiy bash: exiy: command not found (base) [ehspector@dn051 install]$ exit exit srun: error: dn051: task 0: Exited with exit code 127 (base) [ehspector@milan1 dock]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ mkdir test (base) [ehspector@milan1 AMS_536]$ mkdir test mkdir: cannot create directory ‘test’: File exists (base) [ehspector@milan1 AMS_536]$ mkdir move (base) [ehspector@milan1 AMS_536]$ mv test/ move/ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt move Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ rm -r move (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd class_project/ (base) [ehspector@milan1 class_project]$ ls (base) [ehspector@milan1 class_project]$ cd T -bash: cd: T: No such file or directory (base) [ehspector@milan1 class_project]$ ls (base) [ehspector@milan1 class_project]$ cd .. (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26 003_gridbox 006_footprint 009_rescore Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan1 Robs_new_2w26]$ ls 000_test 002_spheres 004_dock 006_ga_lib 001_structure 003_grid 005_analysis 007_ga_run1 (base) [ehspector@milan1 Robs_new_2w26]$ cd .. (base) [ehspector@milan1 2w26]$ mkdir ga_calc (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_new_2w26 002_surface_spheres 005_dock 008_cartesian_min ga_calc test4.tar 003_gridbox 006_footprint 009_rescore Robs_2w26 (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ vi N (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/ (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan1 Robs_new_2w26]$ ls 000_test 002_spheres 004_dock 006_ga_lib 001_structure 003_grid 005_analysis 007_ga_run1 (base) [ehspector@milan1 Robs_new_2w26]$ cd 006_ga_lib/ (base) [ehspector@milan1 006_ga_lib]$ ls 01lib.sh 2W26.fraglib.out 2W26_fragout_scored.mol2 02combine.sh 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26.fraglib.in 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 unique_full_sorted_fraglib.dat 2W26.fraglib.log 2W26_fraglib_torenv.dat (base) [ehspector@milan1 006_ga_lib]$ vi 2W26.fraglib.in (base) [ehspector@milan1 006_ga_lib]$ cd .. (base) [ehspector@milan1 Robs_new_2w26]$ cd .. (base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/006_ga_lib/2W26.fraglib.in ga_calc/2w26_fraglib.in (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_new_2w26 002_surface_spheres 005_dock 008_cartesian_min ga_calc test4.tar 003_gridbox 006_footprint 009_rescore Robs_2w26 (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/ (base) [ehspector@milan1 007_virtual_screen]$ ls virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh (base) [ehspector@milan1 007_virtual_screen]$ cd .. (base) [ehspector@milan1 2w26]$ cp 004_energymin/min.sh ga_calc/lib.sh (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_new_2w26 002_surface_spheres 005_dock 008_cartesian_min ga_calc test4.tar 003_gridbox 006_footprint 009_rescore Robs_2w26 (base) [ehspector@milan1 2w26]$ cd ga_calc/ (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in lib.sh (base) [ehspector@milan1 ga_calc]$ vi lib.sh (base) [ehspector@milan1 ga_calc]$ vi lib.sh (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in (base) [ehspector@milan1 ga_calc]$ cd ../001_structure/ (base) [ehspector@milan1 001_structure]$ ls 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2 (base) [ehspector@milan1 001_structure]$ cd ../ga_calc/ (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in lib.sh (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in (base) [ehspector@milan1 ga_calc]$ bash lib.sh (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in 2W26_fraglib_rigid.mol2 2W26_fraglib_sidechain.mol2 2W26_fraglib_linker.mol2 2W26_fraglib_scaffold.mol2 2W26_fraglib_torenv.dat 2w26_fraglib.out 2w26_fraglib_scored.mol2 lib.sh (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.out (base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_scaffold.mol2 (base) [ehspector@milan1 ga_calc]$ grep -c "lnk" 2W26_fraglib_linker.mol2 51 (base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_linker.mol2 (base) [ehspector@milan1 ga_calc]$ vi py.sh (base) [ehspector@milan1 ga_calc]$ vi lib.sh.sh (base) [ehspector@milan1 ga_calc]$ vi lib.sh (base) [ehspector@milan1 ga_calc]$ vi py.sh (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in 2W26_fraglib_rigid.mol2 2W26_fraglib_sidechain.mol2 py.sh 2W26_fraglib_linker.mol2 2W26_fraglib_scaffold.mol2 2W26_fraglib_torenv.dat 2w26_fraglib.out 2w26_fraglib_scored.mol2 lib.sh (base) [ehspector@milan1 ga_calc]$ vi py.sh (base) [ehspector@milan1 ga_calc]$ module load python (base) [ehspector@milan1 ga_calc]$ bash py.sh (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat (base) [ehspector@milan1 ga_calc]$ cd .. (base) [ehspector@milan1 2w26]$ mkdir ga_run (base) [ehspector@milan1 2w26]$ cd ga_run/ (base) [ehspector@milan1 ga_run]$ ls (base) [ehspector@milan1 ga_run]$ touch 2w26_ga.in (base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in

DOCK v6.12

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic

Genetic Algorithm Recombination Parameters

                                            ga_molecule_file [ga_molecule_file.mol2] ():../001_structure/2w26_ligand_H_cH.mol2
                                                ga_utilities [no] (yes no):
                                    ga_fraglib_scaffold_file [fraglib_scaffold.mol2] ():
                                      ga_fraglib_linker_file [fraglib_linker.mol2] ():
                                   ga_fraglib_sidechain_file [fraglib_sidechain.mol2] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
                                             ga_torenv_table [fraglib_torenv.dat] ():../ga_calc/unique_full_sorted_fraglib.dat
                                          ga_max_generations [100] ():5
                                                 ga_xover_on [yes] (yes no):
                               ga_xover_sampling_method_rand [yes] (yes no):
                                                ga_xover_max [150] ():
                                           ga_bond_tolerance [0.5] ():
                                             ga_angle_cutoff [0.14] ():
                                            ga_check_overlap [no] (yes no):
                                          ga_mutate_addition [yes] (yes no):
                                          ga_mutate_deletion [yes] (yes no):
                                      ga_mutate_substitution [yes] (yes no):
                                       ga_mutate_replacement [yes] (yes no):
                                           ga_mutate_parents [no] (yes no):yes
                                                ga_pmut_rate [0.3] ():
                                                ga_omut_rate [0.7] ():
                                           ga_max_mut_cycles [5] ():
                                      ga_mut_sampling_method [rand] (rand | graph):
                                         ga_num_random_picks [15] ():
                                            ga_max_root_size [5] ():
                                            ga_energy_cutoff [100] ():
                                       ga_heur_unmatched_num [1] ():
                                        ga_heur_matched_rmsd [0.5] ():
                                        ga_constraint_mol_wt [500] ():
                                       ga_constraint_rot_bon [10] ():
                                      ga_constraint_H_accept [10] ():
                                         ga_constraint_H_don [5] ():
                                 ga_constraint_formal_charge [2] ():
                                            ga_ensemble_size [200] ():100
                                         ga_selection_method [elitism] (elitism | tournament | roulette):
                                         ga_elitism_combined [yes] (yes no):
                                           ga_elitism_option [max] (percent | number | max):
                            ga_max_num_gen_with_no_crossover [25] ():
                                          ga_name_identifier [ga] ():
                                            ga_output_prefix [ga_output] ():2w26_ga

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Database Filter Parameters

                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):no

Bump Filter Parameters

                                                 bump_filter [no] (yes no):

Master Score Parameters

                                             score_molecules [yes] (yes no):

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):no

GIST Score Parameters

                                          gist_score_primary [no] (yes no):

MultiGrid Score Parameters

                                     multigrid_score_primary [no] (yes no):

Dock3.5 Score Parameters

                                       dock3.5_score_primary [no] (yes no):

Continuous Energy Score Parameters

                                    continuous_score_primary [no] (yes no):

Footprint Similarity Score Parameters

                          footprint_similarity_score_primary [no] (yes no):

Pharmacophore Similarity Score Parameters

                                 pharmacophore_score_primary [no] (yes no):

Hbond Energy Score Parameters

                                         hbond_score_primary [no] (yes no):

Internal Energy Score Parameters

                               internal_energy_score_primary [no] (yes no):

Descriptor Score Parameters

                                    descriptor_score_primary [no] (yes no):

Zou GB/SA Score Parameters

                                      gbsa_zou_score_primary [no] (yes no):

Hawkins GB/SA Score Parameters

                                  gbsa_hawkins_score_primary [no] (yes no):

SASA Score Parameters

                                          SASA_score_primary [no] (yes no):

Amber Score Parameters

                                         amber_score_primary [no] (yes no):

Error: No scoring function selected for the primary score. Program will now terminate.

(base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in (base) [ehspector@milan1 ga_run]$ ls 2w26_ga.in (base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in (base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in

DOCK v6.12

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic

Genetic Algorithm Recombination Parameters

                                            ga_molecule_file [ga_molecule_file.mol2] ():^C

(base) [ehspector@milan1 ga_run]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_2w26 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_new_2w26 003_gridbox 006_footprint 009_rescore ga_run test4.tar (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ bash commands.txt (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt protein Tutorials (base) [ehspector@milan1 AMS_536]$ cd protein/ (base) [ehspector@milan1 protein]$ ls 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min (base) [ehspector@milan1 protein]$ cd .. (base) [ehspector@milan1 AMS_536]$ rm -r protein/ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_2w26 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_new_2w26 003_gridbox 006_footprint 009_rescore ga_run test4.tar (base) [ehspector@milan1 2w26]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan2 ~]$ cd AMS_536/ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run/ (base) [ehspector@milan2 ga_run]$ ls 2w26_ga.in 2w26_ga_lib.in (base) [ehspector@milan2 ga_run]$ vi 2w26_ga_lib.in (base) [ehspector@milan2 ga_run]$ cd .. (base) [ehspector@milan2 2w26]$ cd Robs_new_2w26/ (base) [ehspector@milan2 Robs_new_2w26]$ cd 007_ga_run1/ (base) [ehspector@milan2 007_ga_run1]$ ls 2W26_ga.in 2W26_ga.restart0000.mol2 2W26_ga.restart0002.mol2 2W26_ga.restart0004.mol2 2W26_ga.out 2W26_ga.restart0001.mol2 2W26_ga.restart0003.mol2 2W26_ga.restart0005.mol2 (base) [ehspector@milan2 007_ga_run1]$ vi 2W26_ga.in (base) [ehspector@milan2 007_ga_run1]$ cd .. (base) [ehspector@milan2 Robs_new_2w26]$ ls 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1 (base) [ehspector@milan2 Robs_new_2w26]$ cd .. (base) [ehspector@milan2 2w26]$ cd ga_run/ (base) [ehspector@milan2 ga_run]$ ls 2w26_ga.in 2w26_ga_lib.in (base) [ehspector@milan2 ga_run]$ rm 2w26_ga_lib.in (base) [ehspector@milan2 ga_run]$ vi 2w26_ga.in (base) [ehspector@milan2 ga_run]$ rm 2w26_ga.in (base) [ehspector@milan2 ga_run]$ cd .. (base) [ehspector@milan2 2w26]$ cp Robs_new_2w26/007_ga_run1/2W26_ga.in ga_calc/2w26_ga.in (base) [ehspector@milan2 2w26]$ mv ga_calc/2w26_ga.in ga_run/ (base) [ehspector@milan2 2w26]$ mv ga_run/ ga_run_5 (base) [ehspector@milan2 2w26]$ mkdir ga_run_50 (base) [ehspector@milan2 2w26]$ cd ga_run_5 (base) [ehspector@milan2 ga_run_5]$ ls 2w26_ga.in (base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in (base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out (base) [ehspector@milan2 ga_run_5]$ ls 2w26_ga.in 2w26_ga.out (base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.out (base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in (base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out (base) [ehspector@milan2 ga_run_5]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0004.mol2 2w26_ga.in 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0005.mol2 2w26_ga.out (base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.in 2w26_ga_5.in (base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.out 2w26_ga_5.out (base) [ehspector@milan2 ga_run_5]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_5.in 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0005.mol2 2w26_ga_5.out (base) [ehspector@milan2 ga_run_5]$ cd .. (base) [ehspector@milan2 2w26]$ cp ga_run_5/2w26_ga_5.in ga_run_50/2w26_ga_50.in (base) [ehspector@milan2 2w26]$ cp 007_virtual_screen/virtual.sh ga_run_50/ga.sh (base) [ehspector@milan2 2w26]$ cd ga_run_50 (base) [ehspector@milan2 ga_run_50]$ ls 2w26_ga_50.in ga.sh (base) [ehspector@milan2 ga_run_50]$ vi ga.sh (base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in (base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in (base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in (base) [ehspector@milan2 ga_run_50]$ avail PARTITION AVAIL TIMELIMIT NODES STATE NODELIST a100 up 8:00:00 2 mix@ a100-[02,04] a100 up 8:00:00 8 alloc@ a100-[03,05-11] a100 up 8:00:00 1 drain* a100-01 a100-large up 8:00:00 2 mix@ a100-[02,04] a100-large up 8:00:00 8 alloc@ a100-[03,05-11] a100-large up 8:00:00 1 drain* a100-01 a100-long up 2-00:00:00 2 mix@ a100-[02,04] a100-long up 2-00:00:00 8 alloc@ a100-[03,05-11] a100-long up 2-00:00:00 1 drain* a100-01 debug-40core up 1:00:00 2 drain* dn[031,037] debug-40core up 1:00:00 1 drain dn061 debug-40core up 1:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] debug-40core up 1:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] extended-40core up 7-00:00:00 2 drain* dn[031,037] extended-40core up 7-00:00:00 1 drain dn061 extended-40core up 7-00:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] extended-40core up 7-00:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] extended-40core-shared up 3-12:00:00 2 drain* dn[031,037] extended-40core-shared up 3-12:00:00 1 drain dn061 extended-40core-shared up 3-12:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] extended-40core-shared up 3-12:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] extended-96core up 7-00:00:00 1 plnd dg025 extended-96core up 7-00:00:00 1 drng@ dg023 extended-96core up 7-00:00:00 1 mix@ dg039 extended-96core up 7-00:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] extended-96core up 7-00:00:00 1 down* dg009 extended-96core up 7-00:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] extended-96core-shared up 3-12:00:00 1 plnd dg025 extended-96core-shared up 3-12:00:00 1 drng@ dg023 extended-96core-shared up 3-12:00:00 1 mix@ dg039 extended-96core-shared up 3-12:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] extended-96core-shared up 3-12:00:00 1 down* dg009 extended-96core-shared up 3-12:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[046-048] hbm-1tb-long-96core up 2-00:00:00 1 idle xm045 hbm-extended-96core up 7-00:00:00 3 plnd xm[008,021,088] hbm-extended-96core up 7-00:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082] hbm-extended-96core up 7-00:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094] hbm-large-96core up 8:00:00 3 plnd xm[008,021,088] hbm-large-96core up 8:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082] hbm-large-96core up 8:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094] hbm-long-96core up 2-00:00:00 3 plnd xm[008,021,088] hbm-long-96core up 2-00:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082] hbm-long-96core up 2-00:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094] hbm-medium-96core up 12:00:00 3 plnd xm[008,021,088] hbm-medium-96core up 12:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082] hbm-medium-96core up 12:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094] hbm-short-96core up 4:00:00 3 plnd xm[008,021,088] hbm-short-96core up 4:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082] hbm-short-96core up 4:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094] large-40core up 8:00:00 2 drain* dn[031,037] large-40core up 8:00:00 1 drain dn061 large-40core up 8:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] large-40core up 8:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] large-96core up 8:00:00 1 plnd dg025 large-96core up 8:00:00 1 drng@ dg023 large-96core up 8:00:00 1 mix@ dg039 large-96core up 8:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] large-96core up 8:00:00 1 down* dg009 large-96core up 8:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] long-40core up 2-00:00:00 2 drain* dn[031,037] long-40core up 2-00:00:00 1 drain dn061 long-40core up 2-00:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] long-40core up 2-00:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] long-40core-shared up 1-00:00:00 2 drain* dn[031,037] long-40core-shared up 1-00:00:00 1 drain dn061 long-40core-shared up 1-00:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] long-40core-shared up 1-00:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] long-96core up 2-00:00:00 1 plnd dg025 long-96core up 2-00:00:00 1 drng@ dg023 long-96core up 2-00:00:00 1 mix@ dg039 long-96core up 2-00:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] long-96core up 2-00:00:00 1 down* dg009 long-96core up 2-00:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] long-96core-shared up 1-00:00:00 1 plnd dg025 long-96core-shared up 1-00:00:00 1 drng@ dg023 long-96core-shared up 1-00:00:00 1 mix@ dg039 long-96core-shared up 1-00:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] long-96core-shared up 1-00:00:00 1 down* dg009 long-96core-shared up 1-00:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] medium-40core up 12:00:00 2 drain* dn[031,037] medium-40core up 12:00:00 1 drain dn061 medium-40core up 12:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] medium-40core up 12:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] medium-96core up 12:00:00 1 plnd dg025 medium-96core up 12:00:00 1 drng@ dg023 medium-96core up 12:00:00 1 mix@ dg039 medium-96core up 12:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] medium-96core up 12:00:00 1 down* dg009 medium-96core up 12:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] ood-short-96core up 4:00:00 1 idle dg038 rn-long-40core up 8-08:00:00 12 idle rn[001-012] short-40core up 4:00:00 2 drain* dn[031,037] short-40core up 4:00:00 1 drain dn061 short-40core up 4:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] short-40core up 4:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] short-40core-shared up 4:00:00 2 drain* dn[031,037] short-40core-shared up 4:00:00 1 drain dn061 short-40core-shared up 4:00:00 10 mix dn[020-021,041-043,052-053,056,059-060] short-40core-shared up 4:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062] short-96core up 4:00:00 1 plnd dg025 short-96core up 4:00:00 1 drng@ dg023 short-96core up 4:00:00 1 mix@ dg039 short-96core up 4:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] short-96core up 4:00:00 1 down* dg009 short-96core up 4:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] short-96core-shared up 4:00:00 1 plnd dg025 short-96core-shared up 4:00:00 1 drng@ dg023 short-96core-shared up 4:00:00 1 mix@ dg039 short-96core-shared up 4:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040] short-96core-shared up 4:00:00 1 down* dg009 short-96core-shared up 4:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048] (base) [ehspector@milan2 ga_run_50]$ vi ga.sh

Press ENTER or type command to continue (base) [ehspector@milan2 ga_run_50]$ ls 2w26_ga_50.in ga.sh (base) [ehspector@milan2 ga_run_50]$ vi ga.sh (base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh Submitted batch job 932640 (base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ ^C (base) [ehspector@milan2 ga_run_50]$ vi ga.sh (base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh Submitted batch job 932642 (base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
           932640 short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)

(base) [ehspector@milan2 ga_run_50]$ scancel 932640 (base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932642 ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)

(base) [ehspector@milan2 ga_run_50]$ scancel 932642 (base) [ehspector@milan2 ga_run_50]$ ls 2w26_ga_50.in ga.sh (base) [ehspector@milan2 ga_run_50]$ vi ga.sh (base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh Submitted batch job 932644 (base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932644 ood-short 2w26_ga_ ehspecto  R       0:03      1 dg038

(base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932644 ood-short 2w26_ga_ ehspecto  R       0:07      1 dg038

(base) [ehspector@milan2 ga_run_50]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0003.mol2 2w26_ga_50.in vs_output.txt 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_50.out 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0005.mol2 ga.sh (base) [ehspector@milan2 ga_run_50]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0006.mol2 ga.sh 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_50.in vs_output.txt 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0005.mol2 2w26_ga_50.out (base) [ehspector@milan2 ga_run_50]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0006.mol2 ga.sh 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_50.in vs_output.txt 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0005.mol2 2w26_ga_50.out (base) [ehspector@milan2 ga_run_50]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932644 ood-short 2w26_ga_ ehspecto  R       0:41      1 dg038

(base) [ehspector@milan2 ga_run_50]$ exit logout (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ class (base) [ehspector@milan2 AMS_536]$ vi Notes.txt (base) [ehspector@milan2 AMS_536]$ check

            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           932644 ood-short 2w26_ga_ ehspecto  R       8:17      1 dg038

(base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar ga_run_50 test4.tar 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_2w26 003_gridbox 006_footprint 009_rescore ga_run_5 Robs_new_2w26 (base) [ehspector@milan2 2w26]$ cd ga_run_50/ (base) [ehspector@milan2 ga_run_50]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0008.mol2 2w26_5_ga.restart0016.mol2 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0009.mol2 2w26_5_ga.restart0017.mol2 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0010.mol2 2w26_5_ga.restart0018.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0011.mol2 2w26_ga_50.in 2w26_5_ga.restart0004.mol2 2w26_5_ga.restart0012.mol2 2w26_ga_50.out 2w26_5_ga.restart0005.mol2 2w26_5_ga.restart0013.mol2 ga.sh 2w26_5_ga.restart0006.mol2 2w26_5_ga.restart0014.mol2 vs_output.txt 2w26_5_ga.restart0007.mol2 2w26_5_ga.restart0015.mol2 (base) [ehspector@milan2 ga_run_50]$ exit logout (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan2 ~]$ cd AMS_536/ (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run_50/ (base) [ehspector@milan2 ga_run_50]$ ls 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0019.mol2 2w26_5_ga.restart0038.mol2 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0020.mol2 2w26_5_ga.restart0039.mol2 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0021.mol2 2w26_5_ga.restart0040.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0022.mol2 2w26_5_ga.restart0041.mol2 2w26_5_ga.restart0004.mol2 2w26_5_ga.restart0023.mol2 2w26_5_ga.restart0042.mol2 2w26_5_ga.restart0005.mol2 2w26_5_ga.restart0024.mol2 2w26_5_ga.restart0043.mol2 2w26_5_ga.restart0006.mol2 2w26_5_ga.restart0025.mol2 2w26_5_ga.restart0044.mol2 2w26_5_ga.restart0007.mol2 2w26_5_ga.restart0026.mol2 2w26_5_ga.restart0045.mol2 2w26_5_ga.restart0008.mol2 2w26_5_ga.restart0027.mol2 2w26_5_ga.restart0046.mol2 2w26_5_ga.restart0009.mol2 2w26_5_ga.restart0028.mol2 2w26_5_ga.restart0047.mol2 2w26_5_ga.restart0010.mol2 2w26_5_ga.restart0029.mol2 2w26_5_ga.restart0048.mol2 2w26_5_ga.restart0011.mol2 2w26_5_ga.restart0030.mol2 2w26_5_ga.restart0049.mol2 2w26_5_ga.restart0012.mol2 2w26_5_ga.restart0031.mol2 2w26_5_ga.restart0050.mol2 2w26_5_ga.restart0013.mol2 2w26_5_ga.restart0032.mol2 2w26_ga_50.in 2w26_5_ga.restart0014.mol2 2w26_5_ga.restart0033.mol2 2w26_ga_50.out 2w26_5_ga.restart0015.mol2 2w26_5_ga.restart0034.mol2 ga.sh 2w26_5_ga.restart0016.mol2 2w26_5_ga.restart0035.mol2 vs_output.txt 2w26_5_ga.restart0017.mol2 2w26_5_ga.restart0036.mol2 2w26_5_ga.restart0018.mol2 2w26_5_ga.restart0037.mol2 (base) [ehspector@milan2 ga_run_50]$ mkdir 50_generations (base) [ehspector@milan2 ga_run_50]$ mv *.mol2 50_generations/ (base) [ehspector@milan2 ga_run_50]$ ls 2w26_ga_50.in 2w26_ga_50.out 50_generations ga.sh vs_output.txt (base) [ehspector@milan2 ga_run_50]$ cd 50_generations/ (base) [ehspector@milan2 50_generations]$ cd .. (base) [ehspector@milan2 ga_run_50]$ cd .. (base) [ehspector@milan2 2w26]$ cd ga_run_5 (base) [ehspector@milan2 ga_run_5]$ mkdir 5_generations (base) [ehspector@milan2 ga_run_5]$ mv *.mol2 5_generations/ (base) [ehspector@milan2 ga_run_5]$ ls 2w26_ga_5.in 2w26_ga_5.out 5_generations (base) [ehspector@milan2 ga_run_5]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tut(base) [ehspect(base) [ehspector@m(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 (base) [ehspector@milan2 Tutorials]$ (base) [ehspector@milan(base) [(base) [ehspector@mila(base) [e(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutorials]$ client_loop: send disconnect: Broken pipe (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ home (base) [ehspector@milan1 espector]$ class (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar ga_run_50 test4.tar 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_2w26 003_gridbox 006_footprint 009_rescore ga_run_5 Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd ga_calc/ (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat (base) [ehspector@milan1 ga_calc]$ vi py.sh (base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base(base) [ehspector@milan1 ga_c(base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat (base) [ehspector@milan1 ga_calc]$ ls 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat (base) [ehspector@milan1 ga_calc]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ cd ga_run_5 (base) [ehspector@milan1 ga_run_5]$ cd .. (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ cd .. (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ cd ../../ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd ../../ (base) [ehspector@milan1 ~]$ ls AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh (base) [ehspector@milan1 ~]$ cd AMS_536/ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd ../ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi commands.txt (base) [ehspector@milan1 AMS_536]$ touch make_folders (base) [ehspector@milan1 AMS_536]$ vi make_folders (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt make_folders Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ bash make_folders make_folders: line 3: folder: Is a directory (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt folder make_folders Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd folder/ (base) [ehspector@milan1 folder]$ ls (base) [ehspector@milan1 folder]$ cd .. (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt folder make_folders Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ rm -r folder/ (base) [ehspector@milan1 AMS_536]$ rm make_folders (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd .. (base) [ehspector@milan1 ~]$ cd AMS_536/ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd .. (base) [ehspector@milan1 ~]$ cd .. (base) [ehspector@milan1 home]$ cd .. (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/ (base) [ehspector@milan1 bin]$ ls am1bcc dock6.mpi multigrid_fp_gen.py sevsolv amberize_complex espgen nchemgrid_GB showbox amberize_ligand grid nchemgrid_SA showsphere amberize_receptor grid-convert parmcal solvgrid antechamber grid-convrds parmchk solvmap atomtype make_phimap prepare_amber.pl sphere_selector bondtype mol2bild.py prepare_rna_amber.pl sphgen chemgrid mol2.py prepgen teLeap combine_torenv.py mopac resp tleap dock6 mopac.sh respgen (base) [ehspector@milan1 bin]$ class (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 2w26/ (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_50 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26 004_energymin 008_cartesian_min ga_run_5 test4.tar (base) [ehspector@milan1 2w26]$ mkdir de_novo (base) [ehspector@milan1 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_5 test4.tar 002_surface_spheres 006_footprint 2025_02_12a_test.tar ga_run_50 003_gridbox 007_virtual_screen de_novo Robs_2w26 004_energymin 008_cartesian_min ga_calc Robs_new_2w26 (base) [ehspector@milan1 2w26]$ cd ../../ (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/ -bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/ -bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory (base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/ -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory (base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/ -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory (base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ cd (base) [ehspector@milan1 ~]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory (base) [ehspector@milan1 ~]$ cd .. (base) [ehspector@milan1 home]$ cd .. (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/ (base) [ehspector@milan1 bin]$ ls am1bcc dock6.mpi multigrid_fp_gen.py sevsolv amberize_complex espgen nchemgrid_GB showbox amberize_ligand grid nchemgrid_SA showsphere amberize_receptor grid-convert parmcal solvgrid antechamber grid-convrds parmchk solvmap atomtype make_phimap prepare_amber.pl sphere_selector bondtype mol2bild.py prepare_rna_amber.pl sphgen chemgrid mol2.py prepgen teLeap combine_torenv.py mopac resp tleap dock6 mopac.sh respgen (base) [ehspector@milan1 bin]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap (base) [ehspector@milan1 bin]$ class (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd .. (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ top

top - 15:15:15 up 1 day, 2:11, 24 users, load average: 0.72, 1.86, 3.46 Tasks: 1532 total, 2 running, 1530 sleeping, 0 stopped, 0 zombie %Cpu(s): 0.8 us, 0.0 sy, 0.0 ni, 99.2 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st MiB Mem : 515564.8 total, 495571.2 free, 20722.4 used, 2594.1 buff/cache MiB Swap: 0.0 total, 0.0 free, 0.0 used. 494842.4 avail Mem

   PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND             
339567 minkwan   20   0  164580  90868   3072 R  99.0   0.0   0:25.66 dock6               
339594 ehspect+  20   0   23432   4096   3072 R   1.6   0.0   0:00.30 top                 
  4135 root      20   0  259340  20196  16384 S   1.0   0.0   4:53.58 NetworkManager      
276537 eswong    20   0  295692  13164   5120 S   0.5   0.0   0:11.35 code-e54c774e0a     
335183 hborche+  20   0 4280208 284596  82944 S   0.5   0.1   0:01.07 cpptools-srv        
     1 root      20   0  172980  12288   9216 S   0.0   0.0   0:40.57 systemd             
     2 root      20   0       0      0      0 S   0.0   0.0   0:00.25 kthreadd            
     3 root       0 -20       0      0      0 I   0.0   0.0   0:00.00 rcu_gp              
     4 root       0 -20       0      0      0 I   0.0   0.0   0:00.00 rcu_par_gp          
     5 root       0 -20       0      0      0 I   0.0   0.0   0:00.00 slub_flushwq        
     6 root       0 -20       0      0      0 I   0.0   0.0   0:00.00 netns               
     8 root       0 -20       0      0      0 I   0.0   0.0   0:00.00 kworker/0:0H-events+
    12 root       0 -20       0      0      0 I   0.0   0.0   0:00.00 mm_percpu_wq        
    13 root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_kthre     
    14 root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_rude_     
    15 root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_trace     
    16 root      20   0       0      0      0 S   0.0   0.0   0:00.38 ksoftirqd/0         
    17 root      20   0       0      0      0 I   0.0   0.0   0:50.41 rcu_preempt         
    18 root      rt   0       0      0      0 S   0.0   0.0   0:00.08 migration/0         
    20 root     -51   0       0      0      0 S   0.0   0.0   0:00.00 idle_inject/0       
    21 root      20   0       0      0      0 S   0.0   0.0   0:00.00 cpuhp/0             
    22 root      20   0       0      0      0 S   0.0   0.0   0:00.00 cpuhp/1

(base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ cd .. (base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan1 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) supremestudier@Evans-MBP Tutorial % ls 1O86 2w26 5EEN folders.txt (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Permission denied, please try again. ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ vi Notes.txt (base) [ehspector@milan1 AMS_536]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ vi ~/.bashrc (base) [ehspector@milan1 ~]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ~]$ home (base) [ehspector@milan2 espector]$ ls 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test (base) [ehspector@milan2 espector]$ class (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ cd Tutorials/ (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 2w26/ (base) [ehspector@milan2 2w26]$ ls 001_structure 005_dock 009_rescore ga_run_5 test4.tar 002_surface_spheres 006_footprint 2025_02_12a_test.tar ga_run_50 003_gridbox 007_virtual_screen de_novo Robs_2w26 004_energymin 008_cartesian_min ga_calc Robs_new_2w26 (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ mkdir de_novo (base) [ehspector@milan2 1O86]$ cd de_novo/ (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 (base) [ehspector@milan2 de_novo]$ touch Du.in (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in

DOCK v6.12

Conformational Sampling Parameters

                                       conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):denovo

De Novo Build Parameters

                                    dn_fraglib_scaffold_file [fraglib_scaffold.mol2] ():
                                      dn_fraglib_linker_file [fraglib_linker.mol2] ():
                                   dn_fraglib_sidechain_file [fraglib_sidechain.mol2] ():
                                    dn_user_specified_anchor [yes] (yes no):
                                      dn_fraglib_anchor_file [fraglib_anchor.mol2] ():
                                             dn_torenv_table [fraglib_torenv.dat] ():
                                          dn_name_identifier [denovo] ():
                                          dn_sampling_method [graph] (ex | rand | graph):
                                          dn_graph_max_picks [30] ():
                                            dn_graph_breadth [3] ():
                                              dn_graph_depth [2] ():
                                        dn_graph_temperature [100.0] ():
                           dn_pruning_conformer_score_cutoff [100.0] ():
                   dn_pruning_conformer_score_scaling_factor [2.0] ():
                                dn_pruning_clustering_cutoff [100.0] ():
                                        dn_remove_duplicates [yes] ( no | yes):
                                   dn_max_duplicates_per_mol [0] ():
                                  dn_write_pruned_duplicates [no] ( no | yes ):
                                         dn_advanced_pruning [yes] (yes | no):
                                     dn_prune_initial_sample [yes] (yes | no):
                                          dn_sample_torsions [yes] (yes | no):
                                dn_prune_individual_torsions [yes] (yes | no):
                                  dn_prune_combined_torsions [yes] (yes | no):
                                    dn_random_root_selection [no] (yes | no):
                                       dn_mol_wt_cutoff_type [soft] (hard | soft):
                                  dn_upper_constraint_mol_wt [550.0] ():500
                                  dn_lower_constraint_mol_wt [0.0] ():
                                           dn_mol_wt_std_dev [35.0] ():
                                       dn_constraint_rot_bon [15] ():
                                 dn_constraint_formal_charge [2.0] ():
                                       dn_heur_unmatched_num [1] ():
                                        dn_heur_matched_rmsd [2.0] ():
                                           dn_unique_anchors [1] ():
                                          dn_max_grow_layers [9] ():
                                            dn_max_root_size [25] ():
                                           dn_max_layer_size [25] ():
                                          dn_max_current_aps [5] ():
                                  dn_max_scaffolds_per_layer [1] ():
                              dn_max_successful_att_per_root [50000] ():
                                        dn_write_checkpoints [yes] (yes no):
                                         dn_write_prune_dump [yes] (yes no):
                                            dn_write_orients [no] (yes no):
                                       dn_write_growth_trees [no] (yes no):
                                            dn_output_prefix [output] ():

Internal Energy Parameters

                                         use_internal_energy [yes] (yes no):
                                     internal_energy_rep_exp [12] ():
                                      internal_energy_cutoff [100.0] ():

Note: Internal energy only includes repulsive VDW for growth and/or minimization.

Database Filter Parameters

                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

                                               orient_ligand [yes] (yes no):no

Bump Filter Parameters

                                                 bump_filter [no] (yes no):

Master Score Parameters

                                             score_molecules [yes] (yes no):

Contact Score Parameters

                                       contact_score_primary [no] (yes no):

Grid Score Parameters

                                          grid_score_primary [yes] (yes no):
                                    grid_score_rep_rad_scale [1] ():
                                        grid_score_vdw_scale [1] ():
                                         grid_score_es_scale [1] ():
                                         grid_lig_efficiency [no] (yes no):
                                      grid_score_grid_prefix [grid] ():

GIST Score Parameters

MultiGrid Score Parameters

Dock3.5 Score Parameters

Continuous Energy Score Parameters

Footprint Similarity Score Parameters

Pharmacophore Similarity Score Parameters

Hbond Energy Score Parameters

Internal Energy Score Parameters

Descriptor Score Parameters

Zou GB/SA Score Parameters

Hawkins GB/SA Score Parameters

SASA Score Parameters

Amber Score Parameters

Simplex Minimization Parameters

                                             minimize_ligand [yes] (yes no):
                                             minimize_anchor [yes] (yes no):
                                    minimize_flexible_growth [yes] (yes no):
                             use_advanced_simplex_parameters [no] (yes no):
                                          simplex_max_cycles [1] ():
                                      simplex_score_converge [0.1] ():
                                      simplex_cycle_converge [1.0] ():
                                          simplex_trans_step [1.0] ():
                                            simplex_rot_step [0.1] ():
                                           simplex_tors_step [10.0] ():
                               simplex_anchor_max_iterations [500] ():
                                 simplex_grow_max_iterations [500] ():
                         simplex_grow_tors_premin_iterations [0] ():
                                           simplex_final_min [no] (yes no):
                                         simplex_random_seed [0] ():
                                       simplex_restraint_min [no] (yes no):

Atom Typing Parameters

                                                  atom_model [all] (all | united):
                                               vdw_defn_file [vdw.defn] ():
                                              flex_defn_file [flex.defn] ():
                                             flex_drive_file [flex_drive.tbl] ():

Initializing De Novo Growth Routines...

Reading the scaffold library from fraglib_scaffold.mol2...Could not open fraglib_scaffold.mol2. Program will terminate.

No such file or directory(base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ cd ../../ (base) [ehspector@milan2 Tutorials]$ cd ../ (base) [ehspector@milan2 AMS_536]$ ls class_project commands.txt Notes.txt Tutorials (base) [ehspector@milan2 AMS_536]$ vi Notes.txt (base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/ (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in (base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2 /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2 (base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99 ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99': No such file or directory (base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw': No such file or directory (base) [ehspector@milan2 de_novo]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/ (base) [ehspector@milan2 parameters]$ ls 1 fraglib_linker.mol2 prot.table.ambcrg.sybH antechamber fraglib_scaffold.mol2 sa_fraglib.dat chem.defn fraglib_sidechain.mol2 screen.in chemgrid fraglib_torenv.dat screen.para chem_match.tbl leap vdw_AMBER_parm94.defn flex.defn na.table.ambcrg vdw_AMBER_parm94.dock3_7.defn flex_drive_mod.tbl pains_table_2019_09_01.dat vdw_AMBER_parm94.dock3_7_one_C_3.defn flex_drive.tbl pains_table.dat vdw_AMBER_parm96.defn flex_just_OH.defn ph4.defn vdw_AMBER_parm99.defn flex_mod2.defn prot.table.ambcrg.ambH vdw_de_novo.defn flex_mod.defn prot.table.ambcrg.pdb3H vdw.parms.amb fraglib_ga_scaffold.mol2 prot.table.ambcrg.pdbH vdw.parms.update.amb (base) [ehspector@milan2 parameters]$ class (base) [ehspector@milan2 AMS_536]$ cd ls -bash: cd: ls: No such file or directory (base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/ (base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out (base) [ehspector@milan2 de_novo]$ vi Du.out (base) [ehspector@milan2 de_novo]$ cd .. (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore de_novo 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 2w26/ga_calc/ (base) [ehspector@milan2 ga_calc]$ ;s -bash: syntax error near unexpected token `;' (base) [ehspector@milan2 ga_calc]$ ls 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat 2W26_fraglib_rigid.mol2 full_fraglib.dat 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat (base) [ehspector@milan2 ga_calc]$ vi 2w26_fraglib.in (base) [ehspector@milan2 ga_calc]$ cd .. (base) [ehspector@milan2 2w26]$ cd .. (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ mkdir ga_calc (base) [ehspector@milan2 1O86]$ cd .. (base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/2w26_fraglib.in 1O86/ga_calc/1O86_fraglib.in (base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/lib.sh 1O86/ga_calc/lib.sh (base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/py.sh 1O86/ga_calc/py.sh (base) [ehspector@milan2 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan2 Tutorials]$ cd 1O86/ (base) [ehspector@milan2 1O86]$ ls 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore de_novo 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt ga_calc (base) [ehspector@milan2 1O86]$ cd ga_calc/ (base) [ehspector@milan2 ga_calc]$ ls 1O86_fraglib.in lib.sh py.sh (base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.in (base) [ehspector@milan2 ga_calc]$ vi lib.sh (base) [ehspector@milan2 ga_calc]$ bash lib.sh (base) [ehspector@milan2 ga_calc]$ ls 1O86_fraglib.in 1O86_fraglib_rigid.mol2 1O86_fraglib_sidechain.mol2 py.sh 1O86_fraglib_linker.mol2 1O86_fraglib_scaffold.mol2 1O86_fraglib_torenv.dat 1O86_fraglib.out 1O86_fraglib_scored.mol2 lib.sh (base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.out (base) [ehspector@milan2 ga_calc]$ ls 1O86_fraglib.in 1O86_fraglib_rigid.mol2 1O86_fraglib_sidechain.mol2 py.sh 1O86_fraglib_linker.mol2 1O86_fraglib_scaffold.mol2 1O86_fraglib_torenv.dat 1O86_fraglib.out 1O86_fraglib_scored.mol2 lib.sh (base) [ehspector@milan2 ga_calc]$ vi py.sh (base) [ehspector@milan2 ga_calc]$ module list Currently Loaded Modulefiles:

1) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack  
2) shared                   4) mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan2 ga_calc]$ module load python (base) [ehspector@milan2 ga_calc]$ bash py.sh (base) [ehspector@milan2 ga_calc]$ ls 1O86_fraglib.in 1O86_fraglib_scored.mol2 lib.sh 1O86_fraglib_linker.mol2 1O86_fraglib_sidechain.mol2 py.sh 1O86_fraglib.out 1O86_fraglib_torenv.dat unique_full_sorted_fraglib.dat 1O86_fraglib_rigid.mol2 full_fraglib.dat 1O86_fraglib_scaffold.mol2 full_sorted_fraglib.dat (base) [ehspector@milan2 ga_calc]$ pwd /gpfs/home/ehspector/AMS_536/Tutorials/1O86/ga_calc (base) [ehspector@milan2 ga_calc]$ cd ../de_novo/ (base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out (base) [ehspector@milan2 de_novo]$ vi Du.out (base) [ehspector@milan2 de_novo]$ vi Du.in (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out Segmentation fault (core dumped) (base) [ehspector@milan2 de_novo]$ la -bash: la: command not found (base) [ehspector@milan2 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2 (base) [ehspector@milan2 de_novo]$ vi Du.out (base) [ehspector@milan2 de_novo]$ vi 1O86_ligand_Du.mol2 (base) [ehspector@milan2 de_novo]$ exit logout Connection to milan.seawulf.stonybrook.edu closed. (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu ehspector@milan.seawulf.stonybrook.edu's password: Duo two-factor login for ehspector

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-9204

Passcode or option (1-1): 1

Pushed a login request to your device... Success. Logging you in... Loading gcc-stack

 Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7

(base) [ehspector@milan1 ~]$ class (base) [ehspector@milan1 AMS_536]$ cd Tutorials/ (base) [ehspector@milan1 Tutorials]$ ls 1O86 2w26 5EEN (base) [ehspector@milan1 Tutorials]$ cd 1O86/de_novo/ (base) [ehspector@milan1 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ vi Du.out (base) [ehspector@milan1 de_novo]$ vi Du.in (base) [ehspector@milan1 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out Segmentation fault (core dumped) (base) [ehspector@milan1 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ vi Du.out (base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ vi Du.out (base) [ehspector@milan1 de_novo]$ vi 1O86_ligand_Du.mol2 (base) [ehspector@milan1 de_novo]$ rm 1O86_ligand_Du.mol2 (base) [ehspector@milan1 de_novo]$ ls Du.in Du.out Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ rm Du.out (base) [ehspector@milan1 de_novo]$ ls 1O86_ligand_Du.mol2 Du.in Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out (base) [ehspector@milan1 de_novo]$ ls 1O86_ligand_Du.mol2 Du.out Du.out.completed.denovo_build.mol2 Du.in Du.out.anchor_1.root_layer_1.mol2 Du.out.denovo_build.mol2 (base) [ehspector@milan1 de_novo]$ vi Du.out (base) [ehspector@milan1 de_novo]$ vi Du.in

conformer_search_type denovo dn_fraglib_scaffold_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2 dn_fraglib_linker_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_linker.mol2 dn_fraglib_sidechain_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2 dn_user_specified_anchor yes dn_fraglib_anchor_file 1O86_ligand_Du.mol2 dn_torenv_table ../ga_calc/unique_full_sorted_fraglib.dat dn_name_identifier denovo dn_sampling_method graph dn_graph_max_picks 30 dn_graph_breadth 3 dn_graph_depth 2 dn_graph_temperature 100.0 dn_pruning_conformer_score_cutoff 100.0 dn_pruning_conformer_score_scaling_factor 2.0 dn_pruning_clustering_cutoff 100.0 dn_remove_duplicates yes dn_max_duplicates_per_mol 0 dn_write_pruned_duplicates no dn_advanced_pruning yes dn_prune_initial_sample yes dn_sample_torsions yes dn_prune_individual_torsions yes dn_prune_combined_torsions yes dn_random_root_selection no dn_mol_wt_cutoff_type soft dn_upper_constraint_mol_wt 1000 dn_lower_constraint_mol_wt 0.0 dn_mol_wt_std_dev 35.0 dn_constraint_rot_bon 15 dn_constraint_formal_charge 2.0 dn_heur_unmatched_num 1 dn_heur_matched_rmsd 2.0 dn_unique_anchors 1 dn_max_grow_layers 1 dn_max_root_size 25 dn_max_layer_size 25 dn_max_current_aps 5 dn_max_scaffolds_per_layer 1 dn_max_successful_att_per_root 50000 dn_write_checkpoints yes dn_write_prune_dump yes dn_write_orients no dn_write_growth_trees no dn_output_prefix Du.out use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 use_database_filter no orient_ligand no bump_filter no score_molecules yes contact_score_primary no grid_score_primary yes grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_lig_efficiency no grid_score_grid_prefix ../003_gridbox/grid minimize_ligand yes minimize_anchor yes minimize_flexible_growth yes use_advanced_simplex_parameters no simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_anchor_max_iterations 500 simplex_grow_max_iterations 500 simplex_grow_tors_premin_iterations 0 simplex_final_min no simplex_random_seed 0 simplex_restraint_min no atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

Difference between revisions of "2025 DOCK tutorial 1 with PDBID 1O86"

Revision as of 12:36, 21 February 2025

Contents

DOCK Tutorial using PDB 1O86

000: Foundations

Chimera

001: Structure Prep

002: Spheres

003: Grid/box

004: Minimization

005: Rigid Docking

006: Flexible Docking

007: Footprint Scoring

008: 5k Virtual Screen

009: Genetic Algorithm Example

010: De Novo Design Example

Selecting a Dummy Atom

Generating a Dummy Atom

Running The Denovo Calculation

> WARNING: A newer version of conda exists. <

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@@ Line 183: / Line 183: @@
 Follow the question tree and use the following sample input file as a template
+Last login: Sat Jan 25 20:39:22 on ttys000
+(base) supremestudier@Evans-MBP ~ % ls
+ay7.cif
+dqx.cif
+-sat-results.csv
+ees.cif
+tj3.cif
+fev.cif
+rfw.cif
+A Hardworking Freshman.txt
+A1_Evan.S.ipynb
+A2_EvanS.ipynb
+AbdulA&YelisvetF_FinalProject_TeenBeachMovieQuiz_.ipynb
+An ambitious kid.txt
+Applications
+Assignment3_EvanS.ipynb
+BE.log
+Beer's Law.xlsx
+Biostats
+CYS_waterbox.pdb
+Customer Data2.xlsx
+Cys.log
+Cysteine_waterbox.pdb
+Data_EvanS.ipynb
+Debugging_EvanS.ipynb
+Desktop
+Documents
+Downloads
+Econ160
+EvanS_W12.ipynb
+Evan_Spector_API_Lab#2.ipynb
+Evan_Spector_API_Lab.ipynb
+Evan_Spector_API_LabMiniProject.ipynb
+Evan_Spector_API_LabMockAPI.ipynb
+Evan_Spector_WebScraping_LabDemos.ipynb
+Evan_Spector_WebScraping_MiniProject.ipynb
+Excel_Evan S.ipynb
+Fate.png
+Final Exercise.xlsx
+Final Project.ipynb
+FinalProject_EvanS-2 - Evan H Spector.ipynb
+FinalProject_EvanS.ipynb
+GS_2.png
+G_waterbox.pdb
+Gall Diameter by Site Boxplot.png
+Game.ipynb
+Graph 1 108.xlsx
+Graph 2 108.xlsx
+Graph 3 108.xlsx
+Guest Speaker Walk through.ipynb
+Hello World.ipynb
+High school Senior Checklist.txt
+Invalid Data.xlsx
+Keq Data.xlsx
+Ksp Data.xlsx
+Lab 2_ Evan S..ipynb
+Lab3_EvanS.ipynb
+Lab5_EvanS.ipynb
+Lab_1 Evan S.ipynb
+Lat.png
+Library
+Linear Regression for Dye.xlsx
+Loops_EvanS.ipynb
+Mambaforge-Darwin-x86_64.
+Methyl Red Excel.xlsx
+Movies
+Music
+NBA_players_2015.csv
+Overdue Customers 2.xlsx
+Oxamide_n2_water.agr
+Peer.ipynb
+Pictures
+Practice.ipynb
+Profile Picture.jpg
+Project.ipynb
+Prototype.ipynb
+Prototype_5.ipynb
+Public
+Quiz Review.ipynb
+README.md
+Reaction 1 Data.xlsx
+Reaction 2 Data.xlsx
+Reaction 3 Data.xlsx
+Reaction 4 Data.xlsx
+Red Cross - Wallet Card - Individual_SD-37055011.pdf
+Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf
+Review Lab_ Evan S..ipynb
+Review3_EvanS.ipynb
+Review_2.ipynb
+SAT__College_Board__2010_School_Level_Results.csv
+Sine and Cosine Curve.ipynb
+Split_2.tga
+SpotifyFinalProject.ipynb
+SulfurCys.agr
+TSLA.csv
+UNL.agr
+Untitled Folder
+Untitled.ipynb
+Untitled1.ipynb
+Untitled2.ipynb
+WAT_O.agr
+Working with OpenPyXL.xlsx
+anaconda3
+eclipse
+eclipse-workspace
+final_project_draft4.ipynb
+helloWorld.py
+install.sh
+introdata.ipynb
+java.log.34001
+java.log.37118
+job_skills.csv
+jupyter_mac.command
+matlab_crash_dump.6196-1
+miniconda3
+multiplot.agr
+opt
+plotting-with-pandas.ipynb
+population-by-country-2020.zip
+population_by_country_2020.csv
+rmsd.agr
+source.venv
+test.encrypted
+test.txt
+twitter-workshop-master.zip
+(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@login.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@login.seawulf.stonybrook.edu's password:
+(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ home
+(base) [ehspector@login1 espector]$ cd ..
+(base) [ehspector@login1 rizzo]$ cd ..
+(base) [ehspector@login1 projects]$ ls
+ABCD                  EssigGroup            MaoGroup             SchedelGroup
+AllamGroup            FarhadzadehGroup      McDonoughGroup       SeeligerGroup
+AllenGroup            FernandezGroup        McGrewGroup          SehgalGroup
+AMS530                FernandezReuterGroup  McKinnonGroup        ShepsonGroup
+AMS536                FrenkelGroup          MehmoodGroup         SherGroup
+AMS598                FutcherGroup          MelikerGroup         SheridanGroup
+AMS691                GenomicsCore          MihalacheGroup       ShilkrotGroup
+Aponte-RiveraGroup    GergenGroup           MirandaGroup         SiegmannGroup
+ArmitageGroup         glimm                 MitchellGroup        SladeGroup
+AssanisGroup          GoblerGroup           MoellerGroup         SmaersGroup
+BEE690                GoldbartGroup         MofakhamGroup        SOC591
+BenchmarkGroup        HCPGroup              MohantyGroup         SOC595
+BenderGroup           HeinzGroup            MollProject          StanacevicGroup
+BernauerGroup         HollisterGroup        molssi               SternGroup
+BialkowskaGroup       HoltGroup             MoutsanidisGroup     SyritsynGroup
+BIO303                hpc_support           MujicaGroup          TakeuchiGroup
+BluesteinGroup        HudsonGroup           NadkarniGroup        TanGroup
+BurguenoGroup         IACSPDPGroup          NMRPIJodeyGroup      TaylorGroup
+CalderGroup           JiaoGroup             NMRPILipshultzGroup  TeraChemGroup
+CanliGroup            JohnsonGroup          NMRPIMingNgaiGroup   Tesse
+CarlsonGroup          JonesBozarthGroup     NMRPIPicartGroup     TestGroup1
+CascanteBonillaGroup  JonesGroup            OjimaGroup           ThackerGroup
+ChangGroup            JonesSkienaGroup      OkeomaGroup          ThakurGroup
+ChapmanGroup          KarzaiGroup           PadillaGroup         ThorneGroup
+CheCastaldoGroup      KeeGroup              PariseGroup          TitleGroup
+ChenGroup             KeeJiaoGroup          PercivalGroup        TsybychevGroup
+ChenXGroup            KellyGroup            PerlmanGroup         VanSnellenbergGroup
+CheungGroup           KhosronejadGroup      PernaGroup           VaskaGroup
+ChowdhuryGroup        KimGroup              PicartGroup          VeeramahGroup
+ChowdhuryRGroup       KirylukGroup          PiretGroup           VitekGroup
+ColleGroup            KodnerGroup           PolakGroup           VonDerLindenGroup
+CollierGroup          KogaGroup             PoonGroup            VorkasGroup
+CSE416                KozakovGroup          PowersGroup          WangGroup
+CSE504                KritzerGroup          PSY610               WanGroup
+CSE519                KrsticGroup           PSY620               WangXGroup
+CSE590                KrsticQuantumGroup    QuantComp            WeinachtGroup
+CSE628                KurcGroup             RahmeGroup           WeinsteinGroup
+DAndreaGroup          LeungGroup            RajputGroup          WeissmanGroup
+DavalosGroup          LevineGroup           RambowGroup          WilsonGroup
+DeLorenzoGroup        LiGroup               RestGroup            WymoreGroup
+DengYasarGroup        LoverdeGroup          ReuterGroup          YeGroup
+DevarajanGroup        LuGroup               RiosGroup            YouGroup
+DheillyGroup          LuhmannGroup          rizzo                ZhangGroup
+DillGroup             LuoGroup              rjh                  ZhanGroup
+DoboliGroup           LynchGroup            RosatiGroup          ZhangYGroup
+DubnauGroup           MaffeiGroup           samples              ZhaoGroup
+EBH370                MaGroup               SampsonCryoEMGroup   ZhouGroup
+EBH381                MakGroup              SampsonGroup         ZhouMedAdvGroup
+EkblomGroup           MallipattuGroup       SamulyakGroup        ZhuGroup
+(base) [ehspector@login1 projects]$ cd AMS536
+(base) [ehspector@login1 AMS536]$ ls
+  2019  2021  2023  2025            zzz.anchors
+  2020  2022  2024  get_anchors.py  zzz.programs
+(base) [ehspector@login1 AMS536]$ cd 2025
+(base) [ehspector@login1 2025]$ ls
+additional_files
+(base) [ehspector@login1 2025]$ cd additional_files/
+(base) [ehspector@login1 additional_files]$ ls
+sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  touch.sh
+(base) [ehspector@login1 additional_files]$ cd ..
+(base) [ehspector@login1 2025]$ cd ..
+(base) [ehspector@login1 AMS536]$ cd 2025
+(base) [ehspector@login1 2025]$ pwd
+/gpfs/projects/AMS536/2025
+(base) [ehspector@login1 2025]$ vi ~/.bashrc
+(base) [ehspector@login1 2025]$ home
+(base) [ehspector@login1 espector]$ source ~/.bashrc
+(base) [ehspector@login1 espector]$ class
+(base) [ehspector@login1 2025]$ home
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP ~ % ls
+ay7.cif
+dqx.cif
+-sat-results.csv
+ees.cif
+tj3.cif
+fev.cif
+rfw.cif
+A Hardworking Freshman.txt
+A1_Evan.S.ipynb
+A2_EvanS.ipynb
+AbdulA&YelisvetF_FinalProject_TeenBeachMovieQuiz_.ipynb
+An ambitious kid.txt
+Applications
+Assignment3_EvanS.ipynb
+BE.log
+Beer's Law.xlsx
+Biostats
+CYS_waterbox.pdb
+Customer Data2.xlsx
+Cys.log
+Cysteine_waterbox.pdb
+Data_EvanS.ipynb
+Debugging_EvanS.ipynb
+Desktop
+Documents
+Downloads
+Econ160
+EvanS_W12.ipynb
+Evan_Spector_API_Lab#2.ipynb
+Evan_Spector_API_Lab.ipynb
+Evan_Spector_API_LabMiniProject.ipynb
+Evan_Spector_API_LabMockAPI.ipynb
+Evan_Spector_WebScraping_LabDemos.ipynb
+Evan_Spector_WebScraping_MiniProject.ipynb
+Excel_Evan S.ipynb
+Fate.png
+Final Exercise.xlsx
+Final Project.ipynb
+FinalProject_EvanS-2 - Evan H Spector.ipynb
+FinalProject_EvanS.ipynb
+GS_2.png
+G_waterbox.pdb
+Gall Diameter by Site Boxplot.png
+Game.ipynb
+Graph 1 108.xlsx
+Graph 2 108.xlsx
+Graph 3 108.xlsx
+Guest Speaker Walk through.ipynb
+Hello World.ipynb
+High school Senior Checklist.txt
+Invalid Data.xlsx
+Keq Data.xlsx
+Ksp Data.xlsx
+Lab 2_ Evan S..ipynb
+Lab3_EvanS.ipynb
+Lab5_EvanS.ipynb
+Lab_1 Evan S.ipynb
+Lat.png
+Library
+Linear Regression for Dye.xlsx
+Loops_EvanS.ipynb
+Mambaforge-Darwin-x86_64.
+Methyl Red Excel.xlsx
+Movies
+Music
+NBA_players_2015.csv
+Overdue Customers 2.xlsx
+Oxamide_n2_water.agr
+Peer.ipynb
+Pictures
+Practice.ipynb
+Profile Picture.jpg
+Project.ipynb
+Prototype.ipynb
+Prototype_5.ipynb
+Public
+Quiz Review.ipynb
+README.md
+Reaction 1 Data.xlsx
+Reaction 2 Data.xlsx
+Reaction 3 Data.xlsx
+Reaction 4 Data.xlsx
+Red Cross - Wallet Card - Individual_SD-37055011.pdf
+Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf
+Review Lab_ Evan S..ipynb
+Review3_EvanS.ipynb
+Review_2.ipynb
+SAT__College_Board__2010_School_Level_Results.csv
+Sine and Cosine Curve.ipynb
+Split_2.tga
+SpotifyFinalProject.ipynb
+SulfurCys.agr
+TSLA.csv
+UNL.agr
+Untitled Folder
+Untitled.ipynb
+Untitled1.ipynb
+Untitled2.ipynb
+WAT_O.agr
+Working with OpenPyXL.xlsx
+anaconda3
+eclipse
+eclipse-workspace
+final_project_draft4.ipynb
+helloWorld.py
+install.sh
+introdata.ipynb
+java.log.34001
+java.log.37118
+job_skills.csv
+jupyter_mac.command
+matlab_crash_dump.6196-1
+miniconda3
+multiplot.agr
+opt
+plotting-with-pandas.ipynb
+population-by-country-2020.zip
+population_by_country_2020.csv
+rmsd.agr
+source.venv
+test.encrypted
+test.txt
+twitter-workshop-master.zip
+(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ home
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd 4s0v/
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ cd no_charge/
+(base) [ehspector@login1 no_charge]$ ls
+s0v_no_hydrogens_no_charges.mol2  gas_2.in  gas_2.out  gas.out_scored.mol2
+(base) [ehspector@login1 no_charge]$ cd ..
+(base) [ehspector@login1 gas_teiger]$ vi no_gas.in
+(base) [ehspector@login1 gas_teiger]$ vi no_gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ cd ..
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd GA_data/
+(base) [ehspector@login1 GA_data]$ ls
+First_gen_data  Last_gen_data
+(base) [ehspector@login1 GA_data]$ cd ..
+(base) [ehspector@login1 4s0v]$ cd gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ home
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd gas_test/
+(base) [ehspector@login1 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@login1 gas_test]$ cd ..
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd 4s0v/
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd s
+-bash: cd: s: No such file or directory
+(base) [ehspector@login1 4s0v]$ cd structure/
+(base) [ehspector@login1 structure]$ ls
+s0v_ligand_hydrogens_charges.mol2        4s0v_no_hydrogens_no_charges.mol2
+s0v_ligand_no_hydrogens_no_charges.mol2  4s0v_protein_with_charges.mol2
+(base) [ehspector@login1 structure]$ cd ..
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd ..
+(base) [ehspector@login1 espector]$ cd gas_test/
+(base) [ehspector@login1 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@login1 gas_test]$ cd gas_f_test/
+(base) [ehspector@login1 gas_f_test]$ ls
+diff.out   gas_0.out_scored.mol2  gas_1.out              gas_50.in   gas_50.out_scored.mol2
+gas_0.out  gas_1.in               gas_1.out_scored.mol2  gas_50.out
+(base) [ehspector@login1 gas_f_test]$ vi gas_1.in
+(base) [ehspector@login1 gas_f_test]$ cd ..
+(base) [ehspector@login1 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@login1 gas_test]$ cd ..
+(base) [ehspector@login1 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ module
+Modules Release 4.0.0 (2017-10-16)
+Usage: module [options] [command] [args ...]
+Loading / Unloading commands:
+  add | load      modulefile [...]  Load modulefile(s)
+  rm | unload     modulefile [...]  Remove modulefile(s)
+  purge                             Unload all loaded modulefiles
+  reload | refresh                  Unload then load all loaded modulefiles
+  switch | swap   [mod1] mod2       Unload mod1 and load mod2
+Listing / Searching commands:
+  list            [-t|-l]           List loaded modules
+  avail   [-d|-L] [-t|-l] [mod ...] List all or matching available modules
+  aliases                           List all module aliases
+  whatis          [modulefile ...]  Print whatis information of modulefile(s)
+  apropos | keyword | search  str   Search all name and whatis containing str
+Collection of modules handling commands:
+  save            [collection|file] Save current module list to collection
+  restore         [collection|file] Restore module list from collection or file
+  saverm          [collection]      Remove saved collection
+  saveshow        [collection|file] Display information about collection
+  savelist        [-t|-l]           List all saved collections
+Shell's initialization files handling commands:
+  initlist                          List all modules loaded from init file
+  initadd         modulefile [...]  Add modulefile to shell init file
+  initrm          modulefile [...]  Remove modulefile from shell init file
+  initprepend     modulefile [...]  Add to beginning of list in init file
+  initswitch      mod1 mod2         Switch mod1 with mod2 from init file
+  initclear                         Clear all modulefiles from init file
+Other commands:
+  help            [modulefile ...]  Print this or modulefile(s) help info
+  display | show  modulefile [...]  Display information about modulefile(s)
+  test            [modulefile ...]  Test modulefile(s)
+  use     [-a|-p] dir [...]         Add dir(s) to MODULEPATH variable
+  unuse           dir [...]         Remove dir(s) from MODULEPATH variable
+  path            modulefile        Print modulefile path
+  paths           modulefile        Print path of matching available modules
+  source          scriptfile [...]  Execute scriptfile(s)
+Switches:
+  -t | --terse    Display output in terse format
+  -l | --long     Display output in long format
+  -d | --default  Only show default versions available
+  -L | --latest   Only show latest versions available
+  -a | --append   Append directory to MODULEPATH
+  -p | --prepend  Prepend directory to MODULEPATH
+Options:
+  -h | --help     This usage info
+  -V | --version  Module version
+  -D | --debug    Enable debug messages
+(base) [ehspector@login1 gas_teiger]$ module list
+Currently Loaded Modulefiles:
+) slurm/17.11.12   2) shared
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ cd ..
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd structure/
+(base) [ehspector@login1 structure]$ ls
+s0v_ligand_hydrogens_charges.mol2        4s0v_no_hydrogens_no_charges.mol2
+s0v_ligand_no_hydrogens_no_charges.mol2  4s0v_protein_with_charges.mol2
+(base) [ehspector@login1 structure]$ cd ..
+(base) [ehspector@login1 4s0v]$ cd gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ cd ..
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ vi gas_teiger/
+(base) [ehspector@login1 4s0v]$ cd gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ cd ..
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd energy_min/
+(base) [ehspector@login1 energy_min]$ ls
+s0v.lig.min_scored.mol2  min.in  min.out
+(base) [ehspector@login1 energy_min]$ cd ..
+(base) [ehspector@login1 4s0v]$ cd ..
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd 4s0v/
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ vi gas_teiger/
+(base) [ehspector@login1 4s0v]$ cd gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ vi gas.
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ cd ..
+(base) [ehspector@login1 4s0v]$ cd surface_spheres/
+(base) [ehspector@login1 surface_spheres]$ ls
+s0v_binding_spheres.sph  4s0v_surface.dms  INSPH  OUTSPH  selected_spheres.sph
+(base) [ehspector@login1 surface_spheres]$ cd ..
+(base) [ehspector@login1 4s0v]$ cd ..
+(base) [ehspector@login1 espector]$ cd gas_test/
+(base) [ehspector@login1 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@login1 gas_test]$ cd ..
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd 4s0v/
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd surface_spheres/
+(base) [ehspector@login1 surface_spheres]$ ls
+s0v_binding_spheres.sph  4s0v_surface.dms  INSPH  OUTSPH  selected_spheres.sph
+(base) [ehspector@login1 surface_spheres]$ cd ..
+(base) [ehspector@login1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login1 4s0v]$ cd gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ vi gas.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
+(base) [ehspector@login1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out
+(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ class
+(base) [ehspector@login2 2025]$ ls
+additional_files
+(base) [ehspector@login2 2025]$ cd additional_files/
+(base) [ehspector@login2 additional_files]$ ls
+sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  touch.sh
+(base) [ehspector@login2 additional_files]$ vi sample_bashrc_4seawulf.txt
+(base) [ehspector@login2 additional_files]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login2 espector]$ cd builds/
+(base) [ehspector@login2 builds]$ cd alpha_branch/
+(base) [ehspector@login2 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@login2 alpha_branch]$ cd install/
+(base) [ehspector@login2 install]$ ls
+bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
+bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
+config.h   gnu.parallel        ibmaix                   Makefile        test
+configure  gnu.parallel.rdkit  intel                    oneapi
+docker     gnu.rdkit           intel.intelmpi.parallel  pgi
+gnu        gnu.valgrind        intel.ip.mkl             rules.h
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ l
+bash: l: command not found...
+(base) [ehspector@login2 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@login2 alpha_branch]$ cd install/
+(base) [ehspector@login2 install]$ ls
+bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
+bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
+config.h   gnu.parallel        ibmaix                   Makefile        test
+configure  gnu.parallel.rdkit  intel                    oneapi
+docker     gnu.rdkit           intel.intelmpi.parallel  pgi
+gnu        gnu.valgrind        intel.ip.mkl             rules.h
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@login2 alpha_branch]$ cd bin/
+(base) [ehspector@login2 bin]$ ls
+dock6  dock6.rdkit
+(base) [ehspector@login2 bin]$ vi dock6.rdkit
+(base) [ehspector@login2 bin]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd src/
+(base) [ehspector@login2 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@login2 src]$ vi Makefile
+(base) [ehspector@login2 src]$ cd rdkit/
+(base) [ehspector@login2 rdkit]$ ls
+boost         boost_1_71_0.tar.gz  eigen-3.3.9.tar.gz  rdkit-Release_2019_09_1
+boost_1_71_0  eigen-3.3.9          Makefile            rdkit-Release_2019_09_1.tar.gz
+(base) [ehspector@login2 rdkit]$ vi Makefile
+(base) [ehspector@login2 rdkit]$ vi Makefile
+(base) [ehspector@login2 rdkit]$ vi Makefile
+(base) [ehspector@login2 rdkit]$ ls
+boost         boost_1_71_0.tar.gz  eigen-3.3.9.tar.gz  rdkit-Release_2019_09_1
+boost_1_71_0  eigen-3.3.9          Makefile            rdkit-Release_2019_09_1.tar.gz
+(base) [ehspector@login2 rdkit]$ module list
+Currently Loaded Modulefiles:
+) slurm/17.11.12   2) shared
+(base) [ehspector@login2 rdkit]$ module load git
+WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
+ /cm/local/apps/environment-modules/4.0.0//bin
+(base) [ehspector@login2 rdkit]$ module list
+Currently Loaded Modulefiles:
+) slurm/17.11.12   2) shared   3) git/2.36.2
+(base) [ehspector@login2 rdkit]$ git branch
+* alpha_branch
+  master
+(base) [ehspector@login2 rdkit]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25
+(base) supremestudier@Evans-MBP Spring_25 % ls
+AMS_500		AMS_537		AMS_691
+AMS_536		AMS_548		CARS_551
+(base) supremestudier@Evans-MBP Spring_25 % cd AMS_691
+(base) supremestudier@Evans-MBP AMS_691 % ls
+AMS691_01.pdf	Projects	Text_book
+(base) supremestudier@Evans-MBP AMS_691 % mkdir Lectures
+(base) supremestudier@Evans-MBP AMS_691 % cd ..
+(base) supremestudier@Evans-MBP Spring_25 % cd AMS_500
+(base) supremestudier@Evans-MBP AMS_500 % ls
+.06.08_hadjiargyrou.pdf
+(base) supremestudier@Evans-MBP AMS_500 % mkdir Materials
+(base) supremestudier@Evans-MBP AMS_500 % mv 2010.06.08_hadjiargyrou.pdf Materials
+(base) supremestudier@Evans-MBP AMS_500 % ls
+Materials
+(base) supremestudier@Evans-MBP AMS_500 % cd ..
+(base) supremestudier@Evans-MBP Spring_25 % cd CARS_551
+(base) supremestudier@Evans-MBP CARS_551 % ls
+(base) supremestudier@Evans-MBP CARS_551 % cd ..
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login2 espector]$ cd gas_test/
+(base) [ehspector@login2 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@login2 gas_test]$ cd ..
+(base) [ehspector@login2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login2 espector]$ cd 4s0v/
+(base) [ehspector@login2 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login2 4s0v]$ cd structure/
+(base) [ehspector@login2 structure]$ ls
+s0v_ligand_hydrogens_charges.mol2        4s0v_no_hydrogens_no_charges.mol2
+s0v_ligand_no_hydrogens_no_charges.mol2  4s0v_protein_with_charges.mol2
+(base) [ehspector@login2 structure]$ cd ..
+(base) [ehspector@login2 4s0v]$ cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
+(base) [ehspector@login2 4s0v]$ cd gas_teiger/
+(base) [ehspector@login2 gas_teiger]$ ls
+s0v_ligand_hydrogens_charges.mol2  gas.out              no_charge  no_gas.out
+gas.in                              gas.out_scored.mol2  no_gas.in  no_gas.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2
+(base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2
+(base) [ehspector@login2 gas_teiger]$ pwd
+/gpfs/projects/rizzo/espector/4s0v/gas_teiger
+(base) [ehspector@login2 gas_teiger]$ ls
+s0v_ligand_hydrogens_charges.mol2  gas.out              no_charge  no_gas.out
+gas.in                              gas.out_scored.mol2  no_gas.in  no_gas.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ cd no_charge/
+(base) [ehspector@login2 no_charge]$ ls
+s0v_no_hydrogens_no_charges.mol2  gas_2.in  gas_2.out  gas.out_scored.mol2
+(base) [ehspector@login2 no_charge]$ vi gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ cd ..
+(base) [ehspector@login2 gas_teiger]$ mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
+(base) [ehspector@login2 gas_teiger]$ cd no_charge/
+(base) [ehspector@login2 no_charge]$ ls
+s0v_ligand_hydrogens_charges.mol2  gas_2.in   gas.out_scored.mol2
+s0v_no_hydrogens_no_charges.mol2   gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@login2 no_charge]$ ls
+s0v_ligand_hydrogens_charges.mol2  gas_2.in   gas.out_scored.mol2
+s0v_no_hydrogens_no_charges.mol2   gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@login2 no_charge]$ ls
+s0v_ligand_hydrogens_charges.mol2  gas_2.in   gas.out_scored.mol2
+s0v_no_hydrogens_no_charges.mol2   gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.out
+(base) [ehspector@login2 no_charge]$ mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
+(base) [ehspector@login2 no_charge]$ ls
+s0v_ligand_hydrogens_no_charges.mol2  gas_2.in   gas.out_scored.mol2
+s0v_no_hydrogens_no_charges.mol2      gas_2.out
+(base) [ehspector@login2 no_charge]$ cd ..
+(base) [ehspector@login2 gas_teiger]$ cd ..
+(base) [ehspector@login2 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
+(base) [ehspector@login2 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/
+(base) [ehspector@login2 no_charge]$ ls
+s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
+s0v.lig.min_scored.mol2               gas_2.out
+s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
+(base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2
+(base) [ehspector@login2 no_charge]$ vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2
+files to edit
+(base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2
+(base) [ehspector@login2 no_charge]$ mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@login2 no_charge]$ ls
+s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
+s0v.lig_no_charge.min_scored.mol2     gas_2.out
+s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
+(base) [ehspector@login2 no_charge]$ vi gas_2.out
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ vi gas.out_scored.mol2
+(base) [ehspector@login2 no_charge]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ cd 4s0v/
+(base) [ehspector@login2 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/
+(base) [ehspector@login2 no_charge]$ vi gas_2.in
+(base) [ehspector@login2 no_charge]$ vi 4s0v.lig_no_charge.min_scored.mol2
+(base) [ehspector@login2 no_charge]$ vi gas_2.out
+(base) [ehspector@login2 no_charge]$ cd ..
+(base) [ehspector@login2 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login2 gas_teiger]$ vi gas.in
+(base) [ehspector@login2 gas_teiger]$ vi gas.out
+(base) [ehspector@login2 gas_teiger]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login2 espector]$ cd 4s0v/
+(base) [ehspector@login2 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@login2 4s0v]$ cd gas_teiger/
+(base) [ehspector@login2 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@login2 gas_teiger]$ vi no_gas.in
+(base) [ehspector@login2 gas_teiger]$ vi no_gas.out
+(base) [ehspector@login2 gas_teiger]$ vi no_gas.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ class
+(base) [ehspector@login1 2025]$ pwd
+/gpfs/projects/AMS536/2025
+(base) [ehspector@login1 2025]$ cd ..
+(base) [ehspector@login1 AMS536]$ vi ~/.bashrc
+(base) [ehspector@login1 AMS536]$ source ~/.bashrc
+WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
+ /cm/local/apps/environment-modules/4.0.0//bin
+(base) [ehspector@login1 AMS536]$ home
+(base) [ehspector@login1 espector]$ class
+(base) [ehspector@login1 2025]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % tutor
+zsh: command not found: tutor
+(base) supremestudier@Evans-MBP Spring_25 % vimtutor
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ class
+(base) [ehspector@login2 2025]$ mkdir ehspector
+mkdir: cannot create directory ‘ehspector’: Permission denied
+(base) [ehspector@login2 2025]$ mkdir ehspector
+(base) [ehspector@login2 2025]$ ls
+additional_files  ehspector  ooreilly
+(base) [ehspector@login2 2025]$ cd ehspector/
+(base) [ehspector@login2 ehspector]$ ls
+(base) [ehspector@login2 ehspector]$ touch file.txt
+(base) [ehspector@login2 ehspector]$ ls
+(base) [ehspector@login2 ehspector]$ cd ..
+(base) [ehspector@login2 2025]$ cd ..
+(base) [ehspector@login2 AMS536]$ cd
+(base) [ehspector@login2 ~]$ ls
+miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@login2 ~]$ mkdir class_project
+(base) [ehspector@login2 ~]$ ls
+class_project  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@login2 ~]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ssh: connect to host login.seawulf.stonybrook.edu port 22: Undefined error: 0
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ home
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd builds/
+(base) [ehspector@login1 builds]$ ls
+alpha_branch  dock6-master  dock6-master.zip  dock6-rdkit
+(base) [ehspector@login1 builds]$ cd alpha_branch/
+(base) [ehspector@login1 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@login1 alpha_branch]$ module load git
+WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
+ /cm/local/apps/environment-modules/4.0.0//bin
+(base) [ehspector@login1 alpha_branch]$ git branch
+* alpha_branch
+  master
+(base) [ehspector@login1 alpha_branch]$ git config --get remote.origin.url
+https://github.com/EvanS-Dock6/dock6.git
+(base) [ehspector@login1 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS_Dock6
+Password for 'https://EvanS_Dock6@github.com':
+remote: Support for password authentication was removed on August 13, 2021.
+remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
+fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
+(base) [ehspector@login1 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+remote: Support for password authentication was removed on August 13, 2021.
+remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
+fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
+(base) [ehspector@login1 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+remote: Enumerating objects: 1129, done.
+remote: Counting objects: 100% (672/672), done.
+remote: Compressing objects: 100% (147/147), done.
+remote: Total 1129 (delta 585), reused 561 (delta 525), pack-reused 457 (from 1)
+Receiving objects: 100% (1129/1129), 1.09 MiB | 13.11 MiB/s, done.
+Resolving deltas: 100% (909/909), completed with 45 local objects.
+From https://github.com/EvanS-Dock6/dock6
+be5c842..2ce698b4  alpha_branch -> origin/alpha_branch
+ce88e6..da80bfc9  master       -> origin/master
+Updating 4be5c842..2ce698b4
+error: Your local changes to the following files would be overwritten by merge:
+	src/dock/dock.cpp
+	src/dock/orient.cpp
+	src/dock/sphere.cpp
+Please commit your changes or stash them before you merge.
+Aborting
+(base) [ehspector@login1 alpha_branch]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+	modified:   src/dock/dock.cpp
+	modified:   src/dock/filter.cpp
+	modified:   src/dock/filter.h
+	modified:   src/dock/gasteiger.cpp
+	modified:   src/dock/orient.cpp
+	modified:   src/dock/sphere.cpp
+	modified:   src/rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 alpha_branch]$ git diff src/dock/dock.cpp
+diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp
+index 81925eac..e447b601 100644
+--- a/src/dock/dock.cpp
++++ b/src/dock/dock.cpp
+@@ -820,7 +820,7 @@ main(int argc, char **argv)
+         if (c_filter.use_database_filter)
+         {
+             //calculate RDKIT-related descriptors for the ligand
+-            c_filter.calc_descriptors(mol);
++            c_filter.calc_descriptors(mol, c_typer);
+             //other descriptors are now computed & printed in amber_typer.cpp
+             //print out the descriptors
+             //cout << c_filter.get_descriptors(mol);
+(base) [ehspector@login1 alpha_branch]$ git diff src/dock/gasteiger.cpp
+diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
+index 5cfba835..3a967b89 100644
+--- a/src/dock/gasteiger.cpp
++++ b/src/dock/gasteiger.cpp
+@@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {
+     //Fochmod
+     //printf("gasteiger mark #1 \n");
+-
++        cout << "The for loop is initiated" << endl;
+     for (int a = 0; a < mol.num_atoms; a++) {
+         //printf("switchloop %d  \n", a);
+         switch (mol.atom_envs[a][1]) {
+@@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {
+                 param_b[a]     = 9.18;
+                 param_c[a]     = 1.88;
+                 param_d[a]     = param_a[a] + param_b[a] + param_c[a];
++                cout << "This is the charge" << endl;
+                 break;
+             case 'B':   //C.2  trtrtr pi
+                 tot_charges[a] = 0.0;
+(base) [ehspector@login1 alpha_branch]$ git diff src/dock/orient.cpp
+diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
+index 92d58f71..2d63fece 100644
+--- a/src/dock/orient.cpp
++++ b/src/dock/orient.cpp
+@@ -461,8 +461,7 @@ Orient::get_spheres()
+     spheres = Active_Site_Spheres :: get_instance();
+     num_spheres = spheres.size();
+-    if (verbose) cout << "Read in " << num_spheres
+-                      << " spheres for orienting." << endl;
++    cout << "Read in " << num_spheres << " spheres for orienting." << endl;
+     // process critical points
+     if (critical_points) {
+(base) [ehspector@login1 alpha_branch]$ git diff src/dock/sphere.cpp
+diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
+index 27641d83..5739a67c 100644
+--- a/src/dock/sphere.cpp
++++ b/src/dock/sphere.cpp
+@@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
+     fclose(sphere_file);
+     return num_spheres;
++
+ }
+(base) [ehspector@login1 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@login1 alpha_branch]$ cd src/dock
+(base) [ehspector@login1 dock]$ vi gasteiger.cpp
+(base) [ehspector@login1 dock]$ git diff gasteiger.cpp
+diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
+index 5cfba835..3a967b89 100644
+--- a/src/dock/gasteiger.cpp
++++ b/src/dock/gasteiger.cpp
+@@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {
+     //Fochmod
+     //printf("gasteiger mark #1 \n");
+-
++        cout << "The for loop is initiated" << endl;
+     for (int a = 0; a < mol.num_atoms; a++) {
+         //printf("switchloop %d  \n", a);
+         switch (mol.atom_envs[a][1]) {
+@@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {
+                 param_b[a]     = 9.18;
+                 param_c[a]     = 1.88;
+                 param_d[a]     = param_a[a] + param_b[a] + param_c[a];
++                cout << "This is the charge" << endl;
+                 break;
+             case 'B':   //C.2  trtrtr pi
+                 tot_charges[a] = 0.0;
+(base) [ehspector@login1 dock]$ vi gasteiger.cpp
+(base) [ehspector@login1 dock]$ git diff gasteiger.cpp
+diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
+index 5cfba835..e82d5397 100644
+--- a/src/dock/gasteiger.cpp
++++ b/src/dock/gasteiger.cpp
+@@ -272,7 +272,6 @@ compute_gast_charges(DOCKMol & mol) {
+     //Fochmod
+     //printf("gasteiger mark #1 \n");
+-
+     for (int a = 0; a < mol.num_atoms; a++) {
+         //printf("switchloop %d  \n", a);
+         switch (mol.atom_envs[a][1]) {
+(base) [ehspector@login1 dock]$ git status gasteiger.cpp
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	modified:   gasteiger.cpp
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 dock]$ vi gasteiger.cpp
+(base) [ehspector@login1 dock]$ git diff gasteiger.cpp
+(base) [ehspector@login1 dock]$ git status gasteiger.cpp
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+nothing to commit, working tree clean
+(base) [ehspector@login1 dock]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    ../../install/test/minimization/minimize7.dockout
+	modified:   dock.cpp
+	modified:   filter.cpp
+	modified:   filter.h
+	modified:   orient.cpp
+	modified:   sphere.cpp
+	modified:   ../rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	lol
+	../rdkit/boost/
+	../rdkit/boost_1_71_0.tar.gz
+	../rdkit/boost_1_71_0/
+	../rdkit/eigen-3.3.9.tar.gz
+	../rdkit/eigen-3.3.9/
+	../rdkit/rdkit-Release_2019_09_1.tar.gz
+	../rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 dock]$ git diff sphere.cpp
+diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
+index 27641d83..5739a67c 100644
+--- a/src/dock/sphere.cpp
++++ b/src/dock/sphere.cpp
+@@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
+     fclose(sphere_file);
+     return num_spheres;
++
+ }
+(base) [ehspector@login1 dock]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % mkdir PHYS_561
+(base) supremestudier@Evans-MBP Spring_25 % cd PHYS_561
+(base) supremestudier@Evans-MBP PHYS_561 % mkdir Readings
+(base) supremestudier@Evans-MBP PHYS_561 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ class
+(base) [ehspector@login2 2025]$ cd
+(base) [ehspector@login2 ~]$ ls
+class_project  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@login2 ~]$ mv class_project/ AMS_536
+(base) [ehspector@login2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@login2 ~]$ cd AMS_536/
+(base) [ehspector@login2 AMS_536]$ ls
+(base) [ehspector@login2 AMS_536]$ mkdir class_work
+(base) [ehspector@login2 AMS_536]$ mkdir class_project
+(base) [ehspector@login2 AMS_536]$ cd ..
+(base) [ehspector@login2 ~]$ cd AMS_536/
+(base) [ehspector@login2 AMS_536]$ pwd
+/gpfs/home/ehspector/AMS_536
+(base) [ehspector@login2 AMS_536]$ vi ~/.bashrc
+(base) [ehspector@login2 AMS_536]$ source ~/.bashrc
+(base) [ehspector@login2 AMS_536]$ home
+(base) [ehspector@login2 espector]$ class
+(base) [ehspector@login2 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@login2 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@login2 AMS_536]$ pwd
+/gpfs/home/ehspector/AMS_536
+(base) [ehspector@login2 AMS_536]$ cd ..
+(base) [ehspector@login2 ~]$ cd ..
+(base) [ehspector@login2 home]$ cd ..
+(base) [ehspector@login2 gpfs]$ cd projects/
+(base) [ehspector@login2 projects]$ ls
+ABCD                  EssigGroup            MaoGroup             SchedelGroup
+AllamGroup            FarhadzadehGroup      McDonoughGroup       SeeligerGroup
+AllenGroup            FernandezGroup        McGrewGroup          SehgalGroup
+AMS530                FernandezReuterGroup  McKinnonGroup        ShepsonGroup
+AMS536                FrenkelGroup          MehmoodGroup         SherGroup
+AMS598                FutcherGroup          MelikerGroup         SheridanGroup
+AMS691                GenomicsCore          MihalacheGroup       ShilkrotGroup
+Aponte-RiveraGroup    GergenGroup           MirandaGroup         SiegmannGroup
+ArmitageGroup         glimm                 MitchellGroup        SladeGroup
+AssanisGroup          GoblerGroup           MoellerGroup         SmaersGroup
+BEE690                GoldbartGroup         MofakhamGroup        SOC591
+BenchmarkGroup        HCPGroup              MohantyGroup         SOC595
+BenderGroup           HeinzGroup            MollProject          StanacevicGroup
+BernauerGroup         HollisterGroup        molssi               SternGroup
+BialkowskaGroup       HoltGroup             MoutsanidisGroup     SyritsynGroup
+BIO303                hpc_support           MujicaGroup          TakeuchiGroup
+BluesteinGroup        HudsonGroup           NadkarniGroup        TanGroup
+BurguenoGroup         IACSPDPGroup          NMRPIJodeyGroup      TaylorGroup
+CalderGroup           JiaoGroup             NMRPILipshultzGroup  TeraChemGroup
+CanliGroup            JohnsonGroup          NMRPIMingNgaiGroup   Tesse
+CarlsonGroup          JonesBozarthGroup     NMRPIPicartGroup     TestGroup1
+CascanteBonillaGroup  JonesGroup            OjimaGroup           ThackerGroup
+ChangGroup            JonesSkienaGroup      OkeomaGroup          ThakurGroup
+ChapmanGroup          KarzaiGroup           PadillaGroup         ThorneGroup
+CheCastaldoGroup      KeeGroup              PariseGroup          TitleGroup
+ChenGroup             KeeJiaoGroup          PercivalGroup        TsybychevGroup
+ChenXGroup            KellyGroup            PerlmanGroup         VanSnellenbergGroup
+CheungGroup           KhosronejadGroup      PernaGroup           VaskaGroup
+ChowdhuryGroup        KimGroup              PicartGroup          VeeramahGroup
+ChowdhuryRGroup       KirylukGroup          PiretGroup           VitekGroup
+ColleGroup            KodnerGroup           PolakGroup           VonDerLindenGroup
+CollierGroup          KogaGroup             PoonGroup            VorkasGroup
+CSE416                KozakovGroup          PowersGroup          WangGroup
+CSE504                KritzerGroup          PSY610               WanGroup
+CSE519                KrsticGroup           PSY620               WangXGroup
+CSE590                KrsticQuantumGroup    QuantComp            WeinachtGroup
+CSE628                KurcGroup             RahmeGroup           WeinsteinGroup
+DAndreaGroup          LeungGroup            RajputGroup          WeissmanGroup
+DavalosGroup          LevineGroup           RambowGroup          WilsonGroup
+DeLorenzoGroup        LiGroup               RestGroup            WymoreGroup
+DengYasarGroup        LoverdeGroup          ReuterGroup          YeGroup
+DevarajanGroup        LuGroup               RiosGroup            YouGroup
+DheillyGroup          LuhmannGroup          rizzo                ZhangGroup
+DillGroup             LuoGroup              rjh                  ZhanGroup
+DoboliGroup           LynchGroup            RosatiGroup          ZhangYGroup
+DubnauGroup           MaffeiGroup           samples              ZhaoGroup
+EBH370                MaGroup               SampsonCryoEMGroup   ZhouGroup
+EBH381                MakGroup              SampsonGroup         ZhouMedAdvGroup
+EkblomGroup           MallipattuGroup       SamulyakGroup        ZhuGroup
+(base) [ehspector@login2 projects]$ cd AMS536
+(base) [ehspector@login2 AMS536]$ cd zzz.programs
+(base) [ehspector@login2 zzz.programs]$ ls
+amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
+de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
+dock6.10         dock6.12         gen-frags-12         VS_libraries
+dock6.10_milan   dock6.12_ams536  old
+(base) [ehspector@login2 zzz.programs]$ cd dock6.12_ams536/
+(base) [ehspector@login2 dock6.12_ams536]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@login2 dock6.12_ams536]$ cd bin/
+(base) [ehspector@login2 bin]$ ls
+am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
+amberize_complex   espgen        nchemgrid_GB          showbox
+amberize_ligand    grid          nchemgrid_SA          showsphere
+amberize_receptor  grid-convert  parmcal               solvgrid
+antechamber        grid-convrds  parmchk               solvmap
+atomtype           make_phimap   prepare_amber.pl      sphere_selector
+bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
+chemgrid           mol2.py       prepgen               teLeap
+combine_torenv.py  mopac         resp                  tleap
+dock6              mopac.sh      respgen
+(base) [ehspector@login2 bin]$ cd
+(base) [ehspector@login2 ~]$ man date
+(base) [ehspector@login2 ~]$
+(base) [ehspector@login2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@login2 ~]$ cd ..
+(base) [ehspector@login2 home]$ cd ..
+(base) [ehspector@login2 gpfs]$ cd projects/AMS536/
+(base) [ehspector@login2 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@login2 AMS536]$ cd 2025/
+(base) [ehspector@login2 2025]$ ls
+additional_files  rotations
+(base) [ehspector@login2 2025]$ cd rotations/
+(base) [ehspector@login2 rotations]$ ls
+aokisamen
+(base) [ehspector@login2 rotations]$ cd ..
+(base) [ehspector@login2 2025]$ cd ..
+(base) [ehspector@login2 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@login2 AMS536]$ cd 2025/
+(base) [ehspector@login2 2025]$ ls
+additional_files  rotations
+(base) [ehspector@login2 2025]$ cd additional_files/
+(base) [ehspector@login2 additional_files]$ ls
+sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  test.txt  touch.sh
+(base) [ehspector@login2 additional_files]$ ls
+sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  test.txt  touch.sh
+(base) [ehspector@login2 additional_files]$ cd ..
+(base) [ehspector@login2 2025]$ ls
+additional_files  rotations
+(base) [ehspector@login2 2025]$ cd ..
+(base) [ehspector@login2 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@login2 AMS536]$ vi junk.txt
+(base) [ehspector@login2 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@login2 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@login2 AMS536]$ cd 2025
+(base) [ehspector@login2 2025]$ ls
+additional_files  rotations  wed_fun.txt
+(base) [ehspector@login2 2025]$ ls
+additional_files  rotations  wed_humpday.txt
+(base) [ehspector@login2 2025]$ cd
+(base) [ehspector@login2 ~]$ cd ../../
+(base) [ehspector@login2 gpfs]$ sinfo
+PARTITION       AVAIL  TIMELIMIT  NODES  STATE NODELIST
+gpu                up    8:00:00      1  drain sn-nvda5
+gpu                up    8:00:00      5  alloc sn-nvda[3-4,6-8]
+p100               up 1-00:00:00      1  alloc cn-nvidia
+gpu-long           up 2-00:00:00      1  drain sn-nvda5
+gpu-long           up 2-00:00:00      5  alloc sn-nvda[3-4,6-8]
+gpu-large          up    8:00:00      1  drain sn-nvda5
+gpu-large          up    8:00:00      5  alloc sn-nvda[3-4,6-8]
+debug-28core       up    1:00:00      1  boot* sn046
+debug-28core       up    1:00:00      6 drain* sn[030-032,107-109]
+debug-28core       up    1:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
+debug-28core       up    1:00:00     12   idle sn[003-004,025-026,043-044,151-156]
+extended-28core    up 7-00:00:00      1  boot* sn046
+extended-28core    up 7-00:00:00      6 drain* sn[030-032,107-109]
+extended-28core    up 7-00:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
+extended-28core    up 7-00:00:00     12   idle sn[003-004,025-026,043-044,151-156]
+large-28core       up    8:00:00      1  boot* sn046
+large-28core       up    8:00:00      6 drain* sn[030-032,107-109]
+large-28core       up    8:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
+large-28core       up    8:00:00     12   idle sn[003-004,025-026,043-044,151-156]
+long-28core        up 2-00:00:00      1  boot* sn046
+long-28core        up 2-00:00:00      6 drain* sn[030-032,107-109]
+long-28core        up 2-00:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
+long-28core        up 2-00:00:00     12   idle sn[003-004,025-026,043-044,151-156]
+medium-28core      up   12:00:00      1  boot* sn046
+medium-28core      up   12:00:00      6 drain* sn[030-032,107-109]
+medium-28core      up   12:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
+medium-28core      up   12:00:00     12   idle sn[003-004,025-026,043-044,151-156]
+short-28core       up    4:00:00      1  boot* sn046
+short-28core       up    4:00:00      6 drain* sn[030-032,107-109]
+short-28core       up    4:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
+short-28core       up    4:00:00     12   idle sn[003-004,025-026,043-044,151-156]
+v100               up 1-00:00:00      2   idle sn-nvda[1-2]
+(base) [ehspector@login2 gpfs]$ alias
+alias class='cd /gpfs/home/ehspector/AMS_536'
+alias egrep='egrep --color=auto'
+alias fgrep='fgrep --color=auto'
+alias grep='grep --color=auto'
+alias home='cd /gpfs/projects/rizzo/espector'
+alias l.='ls -d .* --color=auto'
+alias ll='ls -l --color=auto'
+alias ls='ls --color=auto'
+alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash'
+alias vi='vim'
+alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
+(base) [ehspector@login2 gpfs]$ class
+(base) [ehspector@login2 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@login2 AMS_536]$ cd class_work/
+(base) [ehspector@login2 class_work]$ ls
+(base) [ehspector@login2 class_work]$ touch Notes.txt
+(base) [ehspector@login2 class_work]$ vi Notes.txt
+(base) [ehspector@login2 class_work]$ vi Notes.txt
+(base) [ehspector@login2 class_work]$ vi Notes.txt
+(base) [ehspector@login2 class_work]$ class
+(base) [ehspector@login2 AMS_536]$ cd ..
+(base) [ehspector@login2 ~]$ class
+(base) [ehspector@login2 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@login2 AMS_536]$ cd class_work/
+(base) [ehspector@login2 class_work]$ ls
+Notes.txt
+(base) [ehspector@login2 class_work]$ vi Notes.txt
+(base) [ehspector@login2 class_work]$ vi Notes.txt
+(base) [ehspector@login2 class_work]$ alias
+alias class='cd /gpfs/home/ehspector/AMS_536'
+alias egrep='egrep --color=auto'
+alias fgrep='fgrep --color=auto'
+alias grep='grep --color=auto'
+alias home='cd /gpfs/projects/rizzo/espector'
+alias l.='ls -d .* --color=auto'
+alias ll='ls -l --color=auto'
+alias ls='ls --color=auto'
+alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash'
+alias vi='vim'
+alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
+(base) [ehspector@login2 class_work]$ which dock6
+/gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6
+(base) [ehspector@login2 class_work]$ vi Notes.txt
+(base) [ehspector@login2 class_work]$ vi ~/.bashrc
+(base) [ehspector@login2 class_work]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP PHYS_561 % cd
+(base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_500
+(base) supremestudier@Evans-MBP AMS_500 % ls
+Materials
+(base) supremestudier@Evans-MBP AMS_500 % mkdir Week_2
+(base) supremestudier@Evans-MBP AMS_500 % which python
+/Users/supremestudier/anaconda3/bin/python
+(base) supremestudier@Evans-MBP AMS_500 % pip install polaris-lib
+Collecting polaris-lib
+  Obtaining dependency information for polaris-lib from https://files.pythonhosted.org/packages/5f/69/3a9d76a53ebc41245755a71968e7789c543fe93cb48fff5b0a0a54aff56b/polaris_lib-0.11.6-py3-none-any.whl.metadata
+  Downloading polaris_lib-0.11.6-py3-none-any.whl.metadata (5.9 kB)
+Collecting authlib (from polaris-lib)
+  Obtaining dependency information for authlib from https://files.pythonhosted.org/packages/e8/6a/e83a6c04f8c6014c33d97c135782a55370cf60513f8d9f99f1279c7f9c13/Authlib-1.4.1-py2.py3-none-any.whl.metadata
+  Downloading Authlib-1.4.1-py2.py3-none-any.whl.metadata (3.9 kB)
+Collecting boto3<1.36.0 (from polaris-lib)
+  Obtaining dependency information for boto3<1.36.0 from https://files.pythonhosted.org/packages/65/77/8bbca82f70b062181cf0ae53fd43f1ac6556f3078884bfef9da2269c06a3/boto3-1.35.99-py3-none-any.whl.metadata
+  Downloading boto3-1.35.99-py3-none-any.whl.metadata (6.7 kB)
+Collecting datamol>=0.12.1 (from polaris-lib)
+  Obtaining dependency information for datamol>=0.12.1 from https://files.pythonhosted.org/packages/d4/e7/3df58df1af04dcc694a6c970e7138ba3ec3447a442deb427914438326107/datamol-0.12.5-py3-none-any.whl.metadata
+  Downloading datamol-0.12.5-py3-none-any.whl.metadata (8.0 kB)
+Collecting fastpdb (from polaris-lib)
+  Obtaining dependency information for fastpdb from https://files.pythonhosted.org/packages/ff/e3/be3b68743930f079776cdfa7d6475278c2160f77d2610fd4e98a1ae1c545/fastpdb-1.3.1-cp311-cp311-macosx_10_12_x86_64.whl.metadata
+  Downloading fastpdb-1.3.1-cp311-cp311-macosx_10_12_x86_64.whl.metadata (1.9 kB)
+Requirement already satisfied: fsspec[http] in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (2023.4.0)
+Collecting httpx (from polaris-lib)
+  Obtaining dependency information for httpx from https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl.metadata
+  Downloading httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
+Collecting numcodecs[msgpack]>=0.13.1 (from polaris-lib)
+  Obtaining dependency information for numcodecs[msgpack]>=0.13.1 from https://files.pythonhosted.org/packages/55/9c/5a540965c87f1d553748114734bf808d396e629080d4432e745adee02f09/numcodecs-0.15.0-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading numcodecs-0.15.0-cp311-cp311-macosx_10_9_x86_64.whl.metadata (2.9 kB)
+Requirement already satisfied: numpy<2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (1.24.3)
+Requirement already satisfied: pandas in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (2.0.3)
+Requirement already satisfied: pyarrow<18 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (11.0.0)
+Collecting pydantic>=2 (from polaris-lib)
+  Obtaining dependency information for pydantic>=2 from https://files.pythonhosted.org/packages/f4/3c/8cc1cc84deffa6e25d2d0c688ebb80635dfdbf1dbea3e30c541c8cf4d860/pydantic-2.10.6-py3-none-any.whl.metadata
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+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 73.5/73.5 kB 2.3 MB/s eta 0:00:00
+Downloading httpcore-1.0.7-py3-none-any.whl (78 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.6/78.6 kB 2.4 MB/s eta 0:00:00
+Downloading pyroaring-1.0.0-cp311-cp311-macosx_10_9_x86_64.whl (391 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 391.6/391.6 kB 5.6 MB/s eta 0:00:00
+Downloading typer-0.15.1-py3-none-any.whl (44 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.9/44.9 kB 1.3 MB/s eta 0:00:00
+Downloading annotated_types-0.7.0-py3-none-any.whl (13 kB)
+Downloading biotite-1.1.0-cp311-cp311-macosx_10_9_x86_64.whl (38.7 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.7/38.7 MB 7.7 MB/s eta 0:00:00
+Downloading numpy-1.26.4-cp311-cp311-macosx_10_9_x86_64.whl (20.6 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.6/20.6 MB 7.9 MB/s eta 0:00:00
+Downloading botocore-1.35.99-py3-none-any.whl (13.3 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.3/13.3 MB 8.0 MB/s eta 0:00:00
+Downloading numcodecs-0.15.0-cp311-cp311-macosx_10_9_x86_64.whl (1.6 MB)
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+Downloading s3transfer-0.10.4-py3-none-any.whl (83 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.2/83.2 kB 2.2 MB/s eta 0:00:00
+Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
+Downloading Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB)
+Downloading fasteners-0.19-py3-none-any.whl (18 kB)
+Downloading importlib_resources-6.5.2-py3-none-any.whl (37 kB)
+Downloading loguru-0.7.3-py3-none-any.whl (61 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 1.9 MB/s eta 0:00:00
+Downloading rdkit-2024.9.4-cp311-cp311-macosx_10_15_x86_64.whl (29.9 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.9/29.9 MB 7.8 MB/s eta 0:00:00
+Downloading selfies-2.2.0-py3-none-any.whl (36 kB)
+Downloading biotraj-1.2.2-cp311-cp311-macosx_10_9_x86_64.whl (863 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 863.2/863.2 kB 5.6 MB/s eta 0:00:00
+Downloading scipy-1.15.1-cp311-cp311-macosx_10_13_x86_64.whl (41.4 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 41.4/41.4 MB 7.4 MB/s eta 0:00:00
+Downloading h11-0.14.0-py3-none-any.whl (58 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.3/58.3 kB 1.4 MB/s eta 0:00:00
+Building wheels for collected packages: asciitree
+  Building wheel for asciitree (setup.py) ... done
+  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5032 sha256=24fc75d0363ae85814cc0078da13ef4692220652876b36186c2bc8fd449fbede
+  Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/71/c1/da/23077eb3b87d24d6f3852ed1ed1a1ac2d3c885ad6ebd2b4a07
+Successfully built asciitree
+Installing collected packages: pyroaring, asciitree, typing-extensions, shellingham, selfies, numpy, loguru, importlib-resources, h11, fasteners, deprecated, annotated-types, scipy, rdkit, pydantic-core, numcodecs, httpcore, botocore, zarr, typer, s3transfer, pydantic, httpx, biotraj, authlib, pydantic-settings, datamol, boto3, biotite, fastpdb, polaris-lib
+  Attempting uninstall: typing-extensions
+    Found existing installation: typing_extensions 4.7.1
+    Uninstalling typing_extensions-4.7.1:
+      Successfully uninstalled typing_extensions-4.7.1
+  Attempting uninstall: numpy
+    Found existing installation: numpy 1.24.3
+    Uninstalling numpy-1.24.3:
+      Successfully uninstalled numpy-1.24.3
+  Attempting uninstall: scipy
+    Found existing installation: scipy 1.11.1
+    Uninstalling scipy-1.11.1:
+      Successfully uninstalled scipy-1.11.1
+  Attempting uninstall: botocore
+    Found existing installation: botocore 1.29.76
+    Uninstalling botocore-1.29.76:
+      Successfully uninstalled botocore-1.29.76
+  Attempting uninstall: pydantic
+    Found existing installation: pydantic 1.10.8
+    Uninstalling pydantic-1.10.8:
+      Successfully uninstalled pydantic-1.10.8
+ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
+tables 3.8.0 requires blosc2~=2.0.0, which is not installed.
+tables 3.8.0 requires cython>=0.29.21, which is not installed.
+gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed.
+numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.4 which is incompatible.
+anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible.
+aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible.
+Successfully installed annotated-types-0.7.0 asciitree-0.3.3 authlib-1.4.1 biotite-1.1.0 biotraj-1.2.2 boto3-1.35.99 botocore-1.35.99 datamol-0.12.5 deprecated-1.2.18 fasteners-0.19 fastpdb-1.3.1 h11-0.14.0 httpcore-1.0.7 httpx-0.28.1 importlib-resources-6.5.2 loguru-0.7.3 numcodecs-0.15.0 numpy-1.26.4 polaris-lib-0.11.6 pydantic-2.10.6 pydantic-core-2.27.2 pydantic-settings-2.7.1 pyroaring-1.0.0 rdkit-2024.9.4 s3transfer-0.10.4 scipy-1.15.1 selfies-2.2.0 shellingham-1.5.4 typer-0.15.1 typing-extensions-4.12.2 zarr-2.18.4
+(base) supremestudier@Evans-MBP AMS_500 % polaris login
+[2025-01-31 19:47:50] INFO     Your browser has been opened to visit: external_client.py:149
+                               https://clerk.polarishub.io/oauth/auth
+                               orize?response_type=code&client_id=agQ
+                               P2xVM6JqMHvGc&redirect_uri=https%3A%2F
+                               %2Fpolarishub.io%2Foauth2%2Fcallback&s
+                               cope=profile+email&state=YEjoNaFiIPI4k
+                               rv6quFJFVgB09TcYM&code_challenge=QG1cf
+                               HPgkiyqBUkzPRKUxet5FXo5xZWG21Lh_QXjhSU
+                               &code_challenge_method=S256
+Please enter the authorization token: 013927
+╭─────────────────────────── Traceback (most recent call last) ────────────────────────────╮
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/cli.py:31 in login  │
+│                                                                                          │
+│   28 │   This CLI will use the OAuth2 protocol to gain token-based access to the Polaris │
+│   29 │   """                                                                             │
+│   30 │   client = PolarisHubClient(settings=PolarisHubSettings(_env_file=client_env_file │
+│ ❱ 31 │   client.login(auto_open_browser=auto_open_browser, overwrite=overwrite)          │
+│   32                                                                                     │
+│   33                                                                                     │
+│   34 @app.command(hidden=True)                                                           │
+│                                                                                          │
+│ ╭──────────────────────────────────── locals ─────────────────────────────────────╮      │
+│ │ auto_open_browser = True                                                        │      │
+│ │            client = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │      │
+│ │   client_env_file = '.env'                                                      │      │
+│ │         overwrite = False                                                       │      │
+│ ╰─────────────────────────────────────────────────────────────────────────────────╯      │
+│                                                                                          │
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/client.py:249   │
+│ in login                                                                                 │
+│                                                                                          │
+│   246 │   │   │   auto_open_browser: Whether to automatically open the browser to visit  │
+│   247 │   │   """                                                                        │
+│   248 │   │   if overwrite or self.token is None or not self.ensure_active_token():      │
+│ ❱ 249 │   │   │   self.external_client.interactive_login(overwrite=overwrite, auto_open_ │
+│   250 │   │   │   self.token = self.fetch_token()                                        │
+│   251 │   │                                                                              │
+│   252 │   │   logger.info("You are successfully logged in to the Polaris Hub.")          │
+│                                                                                          │
+│ ╭──────────────────────────────────── locals ─────────────────────────────────────╮      │
+│ │ auto_open_browser = True                                                        │      │
+│ │         overwrite = False                                                       │      │
+│ │              self = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │      │
+│ ╰─────────────────────────────────────────────────────────────────────────────────╯      │
+│                                                                                          │
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │
+│ .py:158 in interactive_login                                                             │
+│                                                                                          │
+│   155 │   │   authorization_code = input("Please enter the authorization token: ")       │
+│   156 │   │                                                                              │
+│   157 │   │   # Step 3: Exchange authorization code for an access token                  │
+│ ❱ 158 │   │   self.fetch_token(code=authorization_code, grant_type="authorization_code") │
+│   159 │   │                                                                              │
+│   160 │   │   logger.info(f"Successfully authenticated to the Polaris Hub as `{self.user │
+│   161                                                                                    │
+│                                                                                          │
+│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
+│ │                  _ = 'YEjoNaFiIPI4krv6quFJFVgB09TcYM'                                │ │
+│ │ authorization_code = '013927'                                                        │ │
+│ │  authorization_url = 'https://clerk.polarishub.io/oauth/authorize?response_type=cod… │ │
+│ │  auto_open_browser = True                                                            │ │
+│ │          overwrite = False                                                           │ │
+│ │               self = <polaris.hub.external_client.ExternalAuthClient object at       │ │
+│ │                      0x1356cad90>                                                    │ │
+│ │     token_is_valid = False                                                           │ │
+│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
+│                                                                                          │
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │
+│ .py:74 in fetch_token                                                                    │
+│                                                                                          │
+│    71 │   def fetch_token(self, **kwargs) -> dict:                                       │
+│    72 │   │   """Light wrapper to automatically pass in the right URL"""                 │
+│    73 │   │   try:                                                                       │
+│ ❱  74 │   │   │   return super().fetch_token(                                            │
+│    75 │   │   │   │   url=self.settings.token_fetch_url, code_verifier=self.code_verifie │
+│    76 │   │   │   )                                                                      │
+│    77 │   │   except OAuth2Error as error:                                               │
+│                                                                                          │
+│ ╭──────────────────────────────────── locals ─────────────────────────────────────╮      │
+│ │ kwargs = {'code': '013927', 'grant_type': 'authorization_code'}                 │      │
+│ │   self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │      │
+│ ╰─────────────────────────────────────────────────────────────────────────────────╯      │
+│                                                                                          │
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:21 │
+│ 7 in fetch_token                                                                         │
+│                                                                                          │
+│   214 │   │   if url is None:                                                            │
+│   215 │   │   │   url = self.metadata.get('token_endpoint')                              │
+│   216 │   │                                                                              │
+│ ❱ 217 │   │   return self._fetch_token(                                                  │
+│   218 │   │   │   url, body=body, auth=auth, method=method,                              │
+│   219 │   │   │   headers=headers, **session_kwargs                                      │
+│   220 │   │   )                                                                          │
+│                                                                                          │
+│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
+│ │                   auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2Cli… │ │
+│ │                          object at 0x136f50190>                                      │ │
+│ │ authorization_response = None                                                        │ │
+│ │                   body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2F… │ │
+│ │             grant_type = 'authorization_code'                                        │ │
+│ │                headers = {                                                           │ │
+│ │                          │   'Accept': 'application/json',                           │ │
+│ │                          │   'Content-Type':                                         │ │
+│ │                          'application/x-www-form-urlencoded;charset=UTF-8'           │ │
+│ │                          }                                                           │ │
+│ │                 kwargs = {                                                           │ │
+│ │                          │   'code_verifier':                                        │ │
+│ │                          'S2qmBfN72W2onFO2So06MzNLUB8yVXmHmp4m9xisHaIUA9zU',         │ │
+│ │                          │   'code': '013927'                                        │ │
+│ │                          }                                                           │ │
+│ │                 method = 'POST'                                                      │ │
+│ │                   self = <polaris.hub.external_client.ExternalAuthClient object at   │ │
+│ │                          0x1356cad90>                                                │ │
+│ │         session_kwargs = {}                                                          │ │
+│ │                  state = None                                                        │ │
+│ │                    url = 'https://clerk.polarishub.io/oauth/token'                   │ │
+│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
+│                                                                                          │
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:37 │
+│ 9 in _fetch_token                                                                        │
+│                                                                                          │
+│   376 │   │   for hook in self.compliance_hook['access_token_response']:                 │
+│   377 │   │   │   resp = hook(resp)                                                      │
+│   378 │   │                                                                              │
+│ ❱ 379 │   │   return self.parse_response_token(resp)                                     │
+│   380 │                                                                                  │
+│   381 │   def _refresh_token(self, url, refresh_token=None, body='', headers=None,       │
+│   382 │   │   │   │   │      auth=None, **kwargs):                                       │
+│                                                                                          │
+│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
+│ │    auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2ClientAuth object   │ │
+│ │           at 0x136f50190>                                                            │ │
+│ │    body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2Fpolarishub.io%2… │ │
+│ │ headers = {                                                                          │ │
+│ │           │   'Accept': 'application/json',                                          │ │
+│ │           │   'Content-Type': 'application/x-www-form-urlencoded;charset=UTF-8'      │ │
+│ │           }                                                                          │ │
+│ │  kwargs = {}                                                                         │ │
+│ │  method = 'POST'                                                                     │ │
+│ │    resp = <Response [401 Unauthorized]>                                              │ │
+│ │    self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90>     │ │
+│ │     url = 'https://clerk.polarishub.io/oauth/token'                                  │ │
+│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
+│                                                                                          │
+│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:35 │
+│ 5 in parse_response_token                                                                │
+│                                                                                          │
+│   352 │   │                                                                              │
+│   353 │   │   token = resp.json()                                                        │
+│   354 │   │   if 'error' in token:                                                       │
+│ ❱ 355 │   │   │   raise self.oauth_error_class(                                          │
+│   356 │   │   │   │   error=token['error'],                                              │
+│   357 │   │   │   │   description=token.get('error_description')                         │
+│   358 │   │   │   )                                                                      │
+│                                                                                          │
+│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
+│ │  resp = <Response [401 Unauthorized]>                                                │ │
+│ │  self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90>       │ │
+│ │ token = {                                                                            │ │
+│ │         │   'error': 'invalid_grant',                                                │ │
+│ │         │   'error_description': 'The provided authorization grant (e.g.,            │ │
+│ │         authorization code, resource owner crede'+156                                │ │
+│ │         }                                                                            │ │
+│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
+╰──────────────────────────────────────────────────────────────────────────────────────────╯
+OAuthError: invalid_grant: The provided authorization grant (e.g., authorization code,
+resource owner credentials) or refresh token is invalid, expired, revoked, does not match
+the redirection URI used in the authorization request, or was issued to another client
+(base) supremestudier@Evans-MBP AMS_500 % polaris login
+[2025-01-31 19:49:32] INFO     Your browser has been opened to visit: external_client.py:149
+                               https://clerk.polarishub.io/oauth/auth
+                               orize?response_type=code&client_id=agQ
+                               P2xVM6JqMHvGc&redirect_uri=https%3A%2F
+                               %2Fpolarishub.io%2Foauth2%2Fcallback&s
+                               cope=profile+email&state=qo1ea4ucZsaZS
+                               OGFfAWK47Skq0G4jU&code_challenge=irfzd
+                               YmRLZliQeiwg2GQYa156QMYqb4zXHNXQJFb0pE
+                               &code_challenge_method=S256
+Please enter the authorization token: MTLLNZK2ZWETMDBMMY0ZMGU5LWJJYZKTZWI5MZYWMDHIOTCZ
+[2025-01-31 19:49:45] INFO     Successfully authenticated to the      external_client.py:160
+                               Polaris Hub as
+                               `evan.spector@stonybrook.edu`! 🎉
+[2025-01-31 19:49:46] INFO     You are successfully logged in to the Polaris   client.py:252
+                               Hub.
+(base) supremestudier@Evans-MBP AMS_500 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+(base) [ehspector@login1 ~]$ home
+(base) [ehspector@login1 espector]$ module list
+Currently Loaded Modulefiles:
+) slurm/17.11.12   2) shared   3) gcc/13.2.0   4) mvapich2/gcc13.2/2.3.7   5) gcc-stack
+(base) [ehspector@login1 espector]$ module load git
+WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
+ /cm/local/apps/environment-modules/4.0.0//bin
+(base) [ehspector@login1 espector]$ git diff
+warning: Not a git repository. Use --no-index to compare two paths outside a working tree
+usage: git diff --no-index [<options>] <path> <path>
+Diff output format options
+    -p, --patch           generate patch
+    -s, --no-patch        suppress diff output
+    -u                    generate patch
+    -U, --unified[=<n>]   generate diffs with <n> lines context
+    -W, --function-context
+                          generate diffs with <n> lines context
+    --raw                 generate the diff in raw format
+    --patch-with-raw      synonym for '-p --raw'
+    --patch-with-stat     synonym for '-p --stat'
+    --numstat             machine friendly --stat
+    --shortstat           output only the last line of --stat
+    -X, --dirstat[=<param1,param2>...]
+                          output the distribution of relative amount of changes for each sub-directory
+    --cumulative          synonym for --dirstat=cumulative
+    --dirstat-by-file[=<param1,param2>...]
+                          synonym for --dirstat=files,param1,param2...
+    --check               warn if changes introduce conflict markers or whitespace errors
+    --summary             condensed summary such as creations, renames and mode changes
+    --name-only           show only names of changed files
+    --name-status         show only names and status of changed files
+    --stat[=<width>[,<name-width>[,<count>]]]
+                          generate diffstat
+    --stat-width <width>  generate diffstat with a given width
+    --stat-name-width <width>
+                          generate diffstat with a given name width
+    --stat-graph-width <width>
+                          generate diffstat with a given graph width
+    --stat-count <count>  generate diffstat with limited lines
+    --compact-summary     generate compact summary in diffstat
+    --binary              output a binary diff that can be applied
+    --full-index          show full pre- and post-image object names on the "index" lines
+    --color[=<when>]      show colored diff
+    --ws-error-highlight <kind>
+                          highlight whitespace errors in the 'context', 'old' or 'new' lines in the diff
+    -z                    do not munge pathnames and use NULs as output field terminators in --raw or --numstat
+    --abbrev[=<n>]        use <n> digits to display object names
+    --src-prefix <prefix>
+                          show the given source prefix instead of "a/"
+    --dst-prefix <prefix>
+                          show the given destination prefix instead of "b/"
+    --line-prefix <prefix>
+                          prepend an additional prefix to every line of output
+    --no-prefix           do not show any source or destination prefix
+    --inter-hunk-context <n>
+                          show context between diff hunks up to the specified number of lines
+    --output-indicator-new <char>
+                          specify the character to indicate a new line instead of '+'
+    --output-indicator-old <char>
+                          specify the character to indicate an old line instead of '-'
+    --output-indicator-context <char>
+                          specify the character to indicate a context instead of ' '
+Diff rename options
+    -B, --break-rewrites[=<n>[/<m>]]
+                          break complete rewrite changes into pairs of delete and create
+    -M, --find-renames[=<n>]
+                          detect renames
+    -D, --irreversible-delete
+                          omit the preimage for deletes
+    -C, --find-copies[=<n>]
+                          detect copies
+    --find-copies-harder  use unmodified files as source to find copies
+    --no-renames          disable rename detection
+    --rename-empty        use empty blobs as rename source
+    --follow              continue listing the history of a file beyond renames
+    -l <n>                prevent rename/copy detection if the number of rename/copy targets exceeds given limit
+Diff algorithm options
+    --minimal             produce the smallest possible diff
+    -w, --ignore-all-space
+                          ignore whitespace when comparing lines
+    -b, --ignore-space-change
+                          ignore changes in amount of whitespace
+    --ignore-space-at-eol
+                          ignore changes in whitespace at EOL
+    --ignore-cr-at-eol    ignore carrier-return at the end of line
+    --ignore-blank-lines  ignore changes whose lines are all blank
+    -I, --ignore-matching-lines <regex>
+                          ignore changes whose all lines match <regex>
+    --indent-heuristic    heuristic to shift diff hunk boundaries for easy reading
+    --patience            generate diff using the "patience diff" algorithm
+    --histogram           generate diff using the "histogram diff" algorithm
+    --diff-algorithm <algorithm>
+                          choose a diff algorithm
+    --anchored <text>     generate diff using the "anchored diff" algorithm
+    --word-diff[=<mode>]  show word diff, using <mode> to delimit changed words
+    --word-diff-regex <regex>
+                          use <regex> to decide what a word is
+    --color-words[=<regex>]
+                          equivalent to --word-diff=color --word-diff-regex=<regex>
+    --color-moved[=<mode>]
+                          moved lines of code are colored differently
+    --color-moved-ws <mode>
+                          how white spaces are ignored in --color-moved
+Other diff options
+    --relative[=<prefix>]
+                          when run from subdir, exclude changes outside and show relative paths
+    -a, --text            treat all files as text
+    -R                    swap two inputs, reverse the diff
+    --exit-code           exit with 1 if there were differences, 0 otherwise
+    --quiet               disable all output of the program
+    --ext-diff            allow an external diff helper to be executed
+    --textconv            run external text conversion filters when comparing binary files
+    --ignore-submodules[=<when>]
+                          ignore changes to submodules in the diff generation
+    --submodule[=<format>]
+                          specify how differences in submodules are shown
+    --ita-invisible-in-index
+                          hide 'git add -N' entries from the index
+    --ita-visible-in-index
+                          treat 'git add -N' entries as real in the index
+    -S <string>           look for differences that change the number of occurrences of the specified string
+    -G <regex>            look for differences that change the number of occurrences of the specified regex
+    --pickaxe-all         show all changes in the changeset with -S or -G
+    --pickaxe-regex       treat <string> in -S as extended POSIX regular expression
+    -O <file>             control the order in which files appear in the output
+    --rotate-to <path>    show the change in the specified path first
+    --skip-to <path>      skip the output to the specified path
+    --find-object <object-id>
+                          look for differences that change the number of occurrences of the specified object
+    --diff-filter [(A|C|D|M|R|T|U|X|B)...[*]]
+                          select files by diff type
+    --output <file>       output to a specific file
+(base) [ehspector@login1 espector]$ git status
+fatal: not a git repository (or any parent up to mount point /)
+Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
+(base) [ehspector@login1 espector]$ git branch
+fatal: not a git repository (or any parent up to mount point /)
+Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ module list
+Currently Loaded Modulefiles:
+) slurm/17.11.12   3) gcc/13.2.0               5) gcc-stack
+) shared           4) mvapich2/gcc13.2/2.3.7   6) git/2.36.2
+(base) [ehspector@login1 espector]$ history
+  make rdkit
+  modue list
+  module list
+  module unload gcc
+  module list
+  module unload mvapich2/gcc13.2/2.3.7
+  module unload gcc-stack
+  module list
+  module load gcc/7.2.0
+  which gcc
+  make rdkitclean
+  make rdkit
+  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
+  vi ~/.bashrc
+  module list
+  ls
+  source ~/.bashrc
+  module list
+  ls
+  vi ~/.bashrc
+  make clean
+  ./configure gnu.rdkit
+  make dock
+  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
+  home
+  cd RDKit/gas/
+  ls
+  sbatch 4s0v_filter.slurm
+  vi 4s0v_filter.slurm
+  sbatch 4s0v_filter.slurm
+  squeue -u ehspector
+  vi 4s0v_filter.slurm
+  squeue -u ehspector
+  cd ..
+  cd 4s0v/
+  cd GA
+  ls
+  cd 4s0v_GA_results/
+  ls
+  vi 4s0v_GA_output.restart0000.mol2
+  vi 4s0v_GA_output.restart0001.mol2
+  cd ..
+  ls
+  cd virtual_screening/
+  ls
+  vi virtual.in
+  squeue -u ehspector
+  cd ..
+  cd RDKit/gas/
+  ls
+  vi filter_out.txt
+  cd ..
+  cd 4s0v/gas_teiger/
+  ls
+  touch gas_rdkit
+  dock6 -i gas_rdkit
+  which dock
+  vi ~/.bashrc
+  source ~/.bashrc
+  which dock
+  which rdkit
+  source ~/.bashrc
+  which dock6
+  which dock6.rdkit
+  vi ~/.bashrc
+  source ~/.bashrc
+  which dock6.rdkit
+  ls
+  dock6.rdkit -i gas_rdkit
+  rm gas_rdkit
+  cd ..
+  cd RDKit/
+  cd gas
+  sbatch 4s0v_filter.slurm
+  squeue -u ehspector
+  ls
+  squeue -u ehspector
+  ls
+  vi output_scored.mol2
+  squeue -u ehspector
+  vi output_scored.mol2
+  cd ..
+  vi output_scored.mol2
+  cd ..
+  cd 4s0v/
+  ls
+  cd GA_data/
+  ls
+  cd ..
+  cd GA
+  ls
+  cd ..
+  cd gas_teiger/
+  ls
+  touch gas_rd.in
+  dock6.rdkit gas_rd.in
+  cd ..
+  cd gas_teiger/
+  dock6 -i gas_rd.in
+  rm gas_rd.in
+  cd ..
+  ls
+  cd ..
+  cd builds/alpha_branch/src/dock
+  vi filter.cpp
+  cd ..
+  cd install/
+  make clean
+  make dock
+  ls
+  ./configure
+  ./configure gnu
+  make -i distclean
+  make dock
+  ./configure
+  ./configure gnu
+  make clean
+  ./configure gnu
+  make dock
+  module unload gcc/7.2.0
+  module load gcc-stack
+  make dock
+  cd ..
+  cd ../..
+  ls
+  cd 4s0v/gas_teiger/
+  ls
+  dock6 -i  gas.in
+  ls
+  vi gas.out_scored.mol2
+  cd ..
+  cd builds/alpha_branch/src/dock
+  ls
+  vi filter.cpp
+  cd ../..
+  cd install/
+  make clean
+  make dock
+  cd ../../..
+  cd 4s0v/gas_teiger/
+  dock6 -i gas.in
+  ls
+  vi gas.out_scored.mol2
+  cd ../..
+  cd builds/alpha_branch/src/dock
+  vi filter.cpp
+  cd ..]
+  cd ..
+  cd install/
+  make clean
+  make dock
+  make clean
+  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
+  home
+  module list
+  cd 4s0v/
+  ls
+  cd GA
+  ls
+  squeue -u ehspector
+  ls
+  cd 4s0v_GA_results/
+  ls
+  cd ..
+  ls
+  cd gas_test/
+  ls
+  vi test.in
+  dock6 -i test.in
+  ls
+  vi test.in
+  dock6 -i test.in
+  cd ..
+  cp 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/
+  ls
+  cd gas_test/
+  ls
+  mkdir gas_f_test
+  ls
+  cd ..
+  cp 4s0v/GA/4s0v_GA_results/4s0v_GA.slurm gas_test/gas_f_test/
+  cd gas_test/
+  mv gas_f_test/4s0v_GA.slurm gas_test
+  ls
+  cd gas_f_test/
+  ls
+  cd ..
+  mv gas_test 4s0v_GA.slurm
+  ls
+  vi 4s0v_GA.slurm
+  vi 4s0v_GA.in
+  cd ..
+  cd 4s0v/GA
+  ls
+  cd 4s0v_fraglib/
+  pwd
+  cd ..
+  cd gas_test/
+  ls
+  vi 4s0v_GA.in
+  cd ..
+  ls
+  cd ..
+  ls
+  cd zzz.programs/
+  ls
+  cd ..
+  cd espector/
+  ls
+  cd gas_test/
+  ls
+  vi 4s0v_GA.in
+  vi 4s0v_GA.slurm
+  vi 4s0v_GA.
+  vi 4s0v_GA.in
+  vi 4s0v_GA.slurm
+  sbatch 4s0v_GA.slurm
+  squeue -u ehspector
+  exit
+  squeue -u ehspector
+  exit
+  home
+  squeue -u ehspector
+  exir
+  exit
+  home
+  squeue -u ehspector
+  ls
+  cd gas_test/
+  ls
+  cd gas_f_test/
+  ls
+  cd ..
+  vi GA.txt
+  cd ..
+  ls
+  cd gas_test/
+  ls
+  vi 4s0v_GA.in
+  cd ..
+  cd 4s0v/GA
+  ls
+  cd 4s0v_
+  cd 4s0v_fraglib/
+  ls
+  cd ..
+  ls
+  cd 4s0v_GA_results/
+  ls
+  vi 4s0v_GA.in
+  cd ..
+  cd 4s0v_fraglib/
+  ls
+  cd ..
+  ls
+  cd ..
+  cd gas_test/
+  ls
+  vi 4s0v_GA.in
+  sbatch 4s0v_GA.slurm
+  squeue -u ehspector
+  home
+  cd gas_test/
+  ls
+  vi GA.txt
+  vi 4s0v_GA.in
+  cd ..
+  vimdiff 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/4s0v_GA.in
+  cd gas_test/
+  vi 4s0v_GA.in
+  sbatch 4s0v_GA.slurm
+  squeue -u ehspector
+  ls
+  vi GA.txt
+  vi 4s0v_GA.in
+  vi GA.txt
+  module list
+  cd ..
+  cd builds/
+  cd alpha_branch/src/dock
+  make clean
+  make dock
+  home
+  ls
+  cd RDKit/
+  ls
+  vi filter.in
+  cd
+  home
+  ls
+  cd RDKit/
+  ls
+  vi output_scored.mol2
+  cd gas/
+  ls
+  vi filter.in
+  cd gas_test/
+  ls
+  vi filter.in
+  vi output_scored.mol2
+  cd ..
+  home
+  ls
+  cd builds/alpha_branch/src/h
+  cd builds/alpha_branch/src/dock
+  cd ..
+  cd install
+  history
+  cd ..
+  cd install/
+  ./configure gnu
+  make clean
+  make dock
+  cd ..
+  ls
+  cd ..
+  ls
+  cd gas_test/
+  ls
+  vi 4s0v_GA.in
+  vi 4s0v_GA.slurm
+  sbatch 4s0v_GA.slurm
+  squeue -u ehspector
+  ls
+  vi GA.txt \
+  vi GA.txt
+  exit
+  home
+  ls
+  cd RDKit/
+  ls
+  cd gas/
+  ls
+  cd ..
+  cd gas_test/
+  ls
+  sbatch 4s0v_GA.slurm
+  vi 4s0v_GA.slurm
+  sbatch 4s0v_GA.slurm
+  squeue -u ehspector
+  ls
+  vi GA.txt
+  home
+  cd builds/alpha_branch/install/
+  make clean
+  ./configure gnu
+  cd ./install
+  make dock
+  cd ..
+  module list
+  module load gcc-stack
+  module list
+  cd ..
+  ls
+  cd gas_test/
+  ls
+  sbatch 4s0v_GA.slurm
+  squeue -u ehspector
+  ls
+  vi 4s0v_GA_output.restart0000.mol2
+  ls
+  module list
+  ls
+  squeue -u ehspector
+  ls
+  squeue -u ehspector
+  exit
+  home
+  ls
+  cd gas_test/
+  ls
+  cd ..
+  cp 4s0v/gas_teiger/gas.in gas_test/gas_f_test/
+  cd gas_test/gas_f_test/
+  ls
+  vi gas.in
+  cd ..
+  pwd
+  cd gas_f_test/
+  vi gas.in
+  dock6 -i gas.in -o gas_0.out
+  ls
+  vi gas.out_scored.mol2
+  vi gas_0.out
+  vi gas.in
+  dock6 -i gas.in -o gas_0.out
+  ls
+  vi gas.out_scored.mol2
+  cd ..
+  vimdiff 4s0v_GA_output.restart0000.mol2 gas_f_test/gas.out_scored.mol2
+  cd ..
+  cd gas_test/
+  vi 4s0v_GA_output.restart0000.mol2
+  cd gas_f_test/
+  ls
+  mv gas.out_scored.mol2 gas_0.out_scored.mol2
+  ls
+  vi gas.in
+  mv gas.in gas_1.in
+  dock6 -i gas_1.in -o gas_1.out
+  ls
+  mv gas.out_scored.mol2 gas_1.out_scored.mol2
+  vi gas_1.out_scored.mol2
+  cd ..
+  vi 4s0v_GA_output.restart0001.mol2
+  vi 4s0v_GA_output.restart0050.mol2
+  cd gas_f_test/
+  ls
+  cp gas_1.in gas_50.out
+  mv gas_50.out gas_50.in
+  vi gas_50.in
+  dock6 -i gas_50.in -o gas_50.out
+  ls
+  mv gas.out_scored.mol2 gas_50.out_scored.mol2
+  vi gas_50.out_scored.mol2
+  cd ..
+  vi 4s0v_GA_output.restart0050.mol2
+  cd gas_f_test/
+  vi gas_50.out_scored.mol2
+  cd ..
+  mkdir gas_RD_tes
+  mv gas_RD_tes/ gas_RD_Test/
+  ls
+  exit
+  make clean
+  make dock
+  cd ..
+  ls
+  home
+  ls
+  cd RDKit/
+  ls
+  vi filter
+  vi filter.in
+  cd gas
+  ls
+  vi filter.
+  vi filter.in
+  cd ..
+  cd RDKit/
+  cd gas/
+  ls
+  cd gas_test/
+  ls
+  cd ..
+  cp RDKit/gas/filter.in gas_test/gas_RD_Test/
+  cd RDKit/
+  ls
+  vi 4s0v_filter.slurm
+  cd ..
+  home
+  cd gas_test/
+  ls
+  cd gas_RD_Test/
+  ls
+  cd ..
+  cd gas_RD_Test/
+  ls
+  cd ..
+  cd gas_f_test/
+  ls
+  vi gas_0.in
+  vi gas_1.in
+  cd ..
+  cd gas_RD_Test/
+  vi filter.in
+  mv filter.in gas.in
+  dock6.rdkit -i gas.in -o gas.out
+  ls
+  vi output_scored.mol2
+  ls
+  vi gas.out
+  vi gas.in
+  dock6.rdkit -i gas.in -o gas.out
+  ls
+  vi gas.out
+  vi gas.in
+  exit
+  home
+  cd builds/alpha_branch/install/
+  make clean
+  ls
+  ./configure gnu.rdkit
+  make dock
+  module list
+  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
+  exit
+  dock6.rdkit -i gas_50.in -o gas_50.out
+  ls
+  grep -wc MOLECULE *.mol2
+  diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2
+  diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
+  vi diff.out
+  vi output_scored.mol2
+  cd ..
+  cd gas_f_test/
+  ls
+  grep -wc MOLECULE gas_50.out_scored.mol2
+  diff gas_50.out_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
+  vi diff.out
+  home
+  vi ~/.bashrc
+  source ~/.bashrc
+  exit
+  home
+  cd gas_test/
+  ls
+  cd gas_RD_Test/
+  ls
+  vi gas.out
+  vi output_scored.mol2
+  vi gas.in
+  vi output_scored.mol2
+  ls
+  cd ..
+  ls
+  grep -wc MOLECULE 4s0v_GA_output.restart0001.mol2
+  cd ..
+  ls
+  cd gas_test/
+  ls
+  cd gas_RD_Test/
+  ls
+  vi gas.out
+  vi output_rejected.mol2
+  cd ..
+  vimdiff 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2
+  diff 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2
+  diff -y 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2
+  cd gas_RD_Test/
+  ls
+  cp gas.in gas_50.in
+  vi gas_50.in
+  dock6.rdkit -i gas_50.in -o gas_50.out
+  dock6.rdkit -i gas.in -o gas.out
+  module list
+  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
+  rd
+  vi ~/.bashrc
+  source ~/.bashrc
+  rd
+  home
+  ls
+  cd gas_test/
+  ls
+  cd gas_f_test/
+  vi diff.out
+  cd ..
+  cd gas_RD_test
+  ls
+  cd gas_RD_Test/
+  ls
+  vi diff.out
+  history
+  ls
+  vi output_scored.mol2
+  cd ..
+  cd gas_f_test/
+  ls
+  vi gas_50.out_scored.mol2
+  home
+  ls
+  cd builds/
+  ls
+  cd ..
+  ls
+  cd gas_test/gas_f_test/
+  ls
+  vi gas_50.out_scored.mol2
+  awk '{print $9}' gas_50.out_scored.mol2
+  :q
+  vi gas_50.out_scored.mol2
+  awk '{print $9}' gas_50.out_scored.mol2
+  :q
+  awk '{print $9}' gas_50.out_scored.mol2 > charges.txt
+  vi charges.txt
+  cd ..
+  cd gas_RD_Test/
+  ls
+  awk '{print $9}' output_scored.mol2 > RD_charges.txt
+  vi RD_charges.txt
+  ls
+  cd ..
+  ls
+  awk '{print $9}' 4s0v_GA_output.restart0050.mol2 > charges.txt
+  vi charges.txt
+  mkdir charge_data.txt
+  ls
+  mv charge_data.txt/ charge_data/
+  ls
+  mv charges.txt charge_data/
+  cd charge_data/
+  ls
+  mv charges.txt original_charges.txt
+  cd ..
+  ls
+  cd gas_f_test/
+  ls
+  mv charges.txt f_charges.txt
+  cd ..
+  mv gas_f_test/f_charges.txt charge_data/
+  ls
+  ls charge_data/
+  ls
+  cd gas_RD_Test/
+  ls
+  cd ..
+  mv gas_RD_Test/RD_charges.txt charge_data/
+  ls
+  exit
+  home
+  cd gas_test/
+  cd charge_data/
+  paste -d "," original_charges.txt f_charges.txt RD_charges.txt > gasteiger_charges.csv
+  vi gasteiger_charges.csv
+  vi original_charges.txt
+  cd ..
+  vi 4s0v_GA_output.restart0050.mol2
+  ls
+  cd charge_data/
+  ls
+  pwd
+  exit
+  home
+  cd ..
+  ls
+  cd AMS536
+  ls
+  cd 2025
+  ls
+  cd additional_files/
+  ls
+  cd ..
+  cd 2025
+  pwd
+  vi ~/.bashrc
+  home
+  source ~/.bashrc
+  class
+  home
+  ls
+  exit
+  home
+  ls
+  cd 4s0v/
+  ls
+  cd gas_teiger/
+  ls
+  cd no_charge/
+  ls
+  cd ..
+  vi no_gas.in
+  vi no_gas.out_scored.mol2
+  cd ..
+  ls
+  cd GA_data/
+  ls
+  cd ..
+  cd gas_teiger/
+  ls
+  vi gas.out_scored.mol2
+  exit
+  home
+  ls
+  cd gas_test/
+  ls
+  cd ..
+  ls
+  cd 4s0v/
+  ls
+  cd s
+  cd structure/
+  ls
+  cd ..
+  ls
+  cd ..
+  cd gas_test/
+  ls
+  cd gas_f_test/
+  ls
+  vi gas_1.in
+  cd ..
+  ls
+  cd ..
+  cd 4s0v/gas_teiger/
+  ls
+  vi gas.in
+  module
+  module list
+  ls
+  cd ..
+  ls
+  cd structure/
+  ls
+  cd ..
+  cd gas_teiger/
+  ls
+  vi gas.in
+  dock6 -i gas.in -o gas.out
+  ls
+  vi gas.out
+  vi gas.out_scored.mol2
+  cd ..
+  ls
+  vi gas_teiger/
+  cd gas_teiger/
+  ls
+  vi gas.in
+  dock6 -i gas.in -o gas.out
+  ls
+  vi gas.out
+  vi gas.out_scored.mol2
+  cd ..
+  ls
+  cd energy_min/
+  ls
+  cd ..
+  ls
+  cd 4s0v/
+  ls
+  vi gas_teiger/
+  cd gas_teiger/
+  vi gas.
+  vi gas.in
+  dock6 -i gas.in -o gas.out
+  ls
+  vi gas.out
+  vi gas.in
+  cd ..
+  cd surface_spheres/
+  ls
+  cd ..
+  cd gas_test/
+  ls
+  cd ..
+  ls
+  cd 4s0v/
+  ls
+  cd surface_spheres/
+  ls
+  cd ..
+  ls
+  cd gas_teiger/
+  ls
+  vi gas.in
+  dock6 -i gas.in -o gas.out
+  ls
+  vi gas.out
+  vi gas.out_scored.mol2
+  vi gas.in
+  dock6 -i gas.in -o gas.out
+  ls
+  vi gas.out
+  vi gas.out_scored.mol2
+  exit
+  home
+  class
+  ls
+  cd additional_files/
+  ls
+  vi sample_bashrc_4seawulf.txt
+  exit
+  home
+  ls
+  cd builds/
+  cd alpha_branch/
+  ls
+  cd install/
+  ls
+  cd ..
+  l
+  ls
+  cd install/
+  ls
+  cd ..
+  ls
+  cd bin/
+  ls
+  vi dock6.rdkit
+  cd ..
+  cd src/
+  ls
+  vi Makefile
+  cd rdkit/
+  ls
+  vi Makefile
+  ls
+  module list
+  module load git
+  module list
+  git branch
+  exit
+  home
+  ls
+  cd gas_test/
+  ls
+  cd ..
+  ls
+  cd 4s0v/
+  ls
+  cd structure/
+  ls
+  cd ..
+  cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
+  cd gas_teiger/
+  ls
+  vi 4s0v_ligand_hydrogens_charges.mol2
+  pwd
+  ls
+  cd no_charge/
+  ls
+  vi gas_2.out
+  vi gas_2.in
+  cd ..
+  mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
+  cd no_charge/
+  ls
+  vi gas_2.in
+  dock6 -i gas_2.in -o gas_2.out
+  vi gas_2.out
+  vi gas_2.in
+  dock6 -i gas_2.in -o gas_2.out
+  ls
+  vi gas_2.out
+  vi gas_2.in
+  dock6 -i gas_2.in -o gas_2.out
+  ls
+  vi gas_2.out
+  mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
+  ls
+  cd ..
+  cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
+  ls
+  cd gas_teiger/no_charge/
+  ls
+  vi 4s0v.lig.min_scored.mol2
+  vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2
+  vi 4s0v.lig.min_scored.mol2
+  mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
+  vi gas_2.in
+  dock6 -i gas_2.in -o gas_2.out
+  ls
+  vi gas_2.out
+  vi gas_2.in
+  vi gas.out_scored.mol2
+  exit
+  home
+  cd 4s0v/
+  ls
+  cd gas_teiger/no_charge/
+  vi gas_2.in
+  vi 4s0v.lig_no_charge.min_scored.mol2
+  vi gas_2.out
+  cd ..
+  ls
+  vi gas.in
+  vi gas.out
+  exit
+  home
+  ls
+  cd 4s0v/
+  ls
+  cd gas_teiger/
+  ls
+  vi no_gas.in
+  vi no_gas.out
+  vi no_gas.out_scored.mol2
+  exit
+  class
+  pwd
+  cd ..
+  vi ~/.bashrc
+  source ~/.bashrc
+  home
+  class
+  exit
+  class
+  mkdir ehspector
+  ls
+  cd ehspector/
+  ls
+  touch file.txt
+  ls
+  cd ..
+  cd
+  ls
+  mkdir class_project
+  ls
+  exit
+  home
+  ls
+  cd builds/
+  ls
+  cd alpha_branch/
+  ls
+  module load git
+  git branch
+  git config --get remote.origin.url
+  git pull
+  git status
+  git diff src/dock/dock.cpp
+  git diff src/dock/gasteiger.cpp
+  git diff src/dock/orient.cpp
+  git diff src/dock/sphere.cpp
+  ls
+  cd src/dock
+  vi gasteiger.cpp
+  git diff gasteiger.cpp
+  vi gasteiger.cpp
+  git diff gasteiger.cpp
+  git status gasteiger.cpp
+  vi gasteiger.cpp
+  git diff gasteiger.cpp
+  git status gasteiger.cpp
+  git status
+  git diff sphere.cpp
+  exit
+  home
+  class
+  cd
+  ls
+  mv class_project/ AMS_536
+  ls
+  cd AMS_536/
+  ls
+  mkdir class_work
+  mkdir class_project
+  cd ..
+  cd AMS_536/
+  pwd
+  vi ~/.bashrc
+  source ~/.bashrc
+  home
+  class
+  ls
+  pwd
+  cd ..
+  cd projects/
+  ls
+  cd AMS536
+  cd zzz.programs
+  ls
+  cd dock6.12_ams536/
+  ls
+  cd bin/
+  ls
+  cd
+  man date
+  ls
+  cd ..
+  cd projects/AMS536/
+  ls
+  cd 2025/
+  ls
+  cd rotations/
+  ls
+  cd ..
+  ls
+  cd 2025/
+  ls
+  cd additional_files/
+  ls
+  cd ..
+  ls
+  cd ..
+  ls
+  vi junk.txt
+  ls
+  cd 2025
+  ls
+  cd
+  cd ../../
+  sinfo
+  alias
+  class
+  ls
+  cd class_work/
+  ls
+  touch Notes.txt
+  vi Notes.txt
+  class
+  cd ..
+  class
+  ls
+  cd class_work/
+  ls
+  vi Notes.txt
+  which dock6
+  vi Notes.txt
+  vi ~/.bashrc
+  exit
+  home
+  module list
+  module load git
+  git diff
+  git status
+  git branch
+  ls
+  module list
+  history
+(base) [ehspector@login1 espector]$ git branch
+fatal: not a git repository (or any parent up to mount point /)
+Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
+(base) [ehspector@login1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login1 espector]$ cd builds/alpha_branch/
+(base) [ehspector@login1 alpha_branch]$ git branch
+* alpha_branch
+  master
+(base) [ehspector@login1 alpha_branch]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+	modified:   src/dock/dock.cpp
+	modified:   src/dock/filter.cpp
+	modified:   src/dock/filter.h
+	modified:   src/dock/orient.cpp
+	modified:   src/dock/sphere.cpp
+	modified:   src/rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 alpha_branch]$ cd src/dock
+(base) [ehspector@login1 dock]$ ;s
+-bash: syntax error near unexpected token `;'
+(base) [ehspector@login1 dock]$ ls
+amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
+amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
+amber_typer.o       fingerprint.h         nab                   score_internal.o
+base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
+base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
+base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
+base_mpi.cpp        fraggraph.o           orient.h              score.o
+base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
+base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
+base_score.cpp      fragment.o            rddrive.h             score_ph4.o
+base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
+base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
+conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
+conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
+conf_gen_ag.o       grid.h                README                score_solvent.h
+conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
+conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
+conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
+conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
+conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
+conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
+conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
+conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
+conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
+conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
+conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
+conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
+conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
+conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
+conf_gen_hdb.o      lol                   score_footprint.h     trace.o
+defreal.h           Makefile              score_footprint.o     utils.cpp
+dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
+dockmol.cpp         master_conf.h         score_gist.h          utils.o
+dockmol.h           master_conf.o         score_gist.o          version.h
+dockmol.o           master_score.cpp      score.h               xlogp.cpp
+dock.o              master_score.h        score_hbond.cpp       xlogp.h
+filter.cpp          master_score.o        score_hbond.h
+filter.h            mem_info.cpp          score_hbond.o
+(base) [ehspector@login1 dock]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    ../../install/test/minimization/minimize7.dockout
+	modified:   dock.cpp
+	modified:   filter.cpp
+	modified:   filter.h
+	modified:   orient.cpp
+	modified:   sphere.cpp
+	modified:   ../rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	lol
+	../rdkit/boost/
+	../rdkit/boost_1_71_0.tar.gz
+	../rdkit/boost_1_71_0/
+	../rdkit/eigen-3.3.9.tar.gz
+	../rdkit/eigen-3.3.9/
+	../rdkit/rdkit-Release_2019_09_1.tar.gz
+	../rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 dock]$ git diff dock.cpp
+diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp
+index 81925eac..e447b601 100644
+--- a/src/dock/dock.cpp
++++ b/src/dock/dock.cpp
+@@ -820,7 +820,7 @@ main(int argc, char **argv)
+         if (c_filter.use_database_filter)
+         {
+             //calculate RDKIT-related descriptors for the ligand
+-            c_filter.calc_descriptors(mol);
++            c_filter.calc_descriptors(mol, c_typer);
+             //other descriptors are now computed & printed in amber_typer.cpp
+             //print out the descriptors
+             //cout << c_filter.get_descriptors(mol);
+(base) [ehspector@login1 dock]$ git diff orient.cpp
+diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
+index 92d58f71..2d63fece 100644
+--- a/src/dock/orient.cpp
++++ b/src/dock/orient.cpp
+@@ -461,8 +461,7 @@ Orient::get_spheres()
+     spheres = Active_Site_Spheres :: get_instance();
+     num_spheres = spheres.size();
+-    if (verbose) cout << "Read in " << num_spheres
+-                      << " spheres for orienting." << endl;
++    cout << "Read in " << num_spheres << " spheres for orienting." << endl;
+     // process critical points
+     if (critical_points) {
+(base) [ehspector@login1 dock]$ vi orient.cpp
+(base) [ehspector@login1 dock]$ vi orient.cpp
+(base) [ehspector@login1 dock]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    ../../install/test/minimization/minimize7.dockout
+	modified:   dock.cpp
+	modified:   filter.cpp
+	modified:   filter.h
+	modified:   orient.cpp
+	modified:   sphere.cpp
+	modified:   ../rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	lol
+	../rdkit/boost/
+	../rdkit/boost_1_71_0.tar.gz
+	../rdkit/boost_1_71_0/
+	../rdkit/eigen-3.3.9.tar.gz
+	../rdkit/eigen-3.3.9/
+	../rdkit/rdkit-Release_2019_09_1.tar.gz
+	../rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 dock]$ cd ..
+(base) [ehspector@login1 src]$ cd rdkit
+(base) [ehspector@login1 rdkit]$ vi Makefile
+(base) [ehspector@login1 rdkit]$ cd ..
+(base) [ehspector@login1 src]$ cd dock
+(base) [ehspector@login1 dock]$ git diff orient.cpp
+diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
+index 92d58f71..ff8d8a36 100644
+--- a/src/dock/orient.cpp
++++ b/src/dock/orient.cpp
+@@ -460,9 +460,9 @@ Orient::get_spheres()
+     spheres = Active_Site_Spheres :: get_instance();
+     num_spheres = spheres.size();
+-
+-    if (verbose) cout << "Read in " << num_spheres
+-                      << " spheres for orienting." << endl;
++
++    // prints the number of spheres that are generated EHS 9/18/23
++    cout << "Read in " << num_spheres << " spheres for orienting." << endl;
+     // process critical points
+     if (critical_points) {
+(base) [ehspector@login1 dock]$ git diff sphere.cpp
+diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
+index 27641d83..5739a67c 100644
+--- a/src/dock/sphere.cpp
++++ b/src/dock/sphere.cpp
+@@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
+     fclose(sphere_file);
+     return num_spheres;
++
+ }
+(base) [ehspector@login1 dock]$ vi sphere.cpp
+(base) [ehspector@login1 dock]$ ls
+amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
+amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
+amber_typer.o       fingerprint.h         nab                   score_internal.o
+base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
+base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
+base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
+base_mpi.cpp        fraggraph.o           orient.h              score.o
+base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
+base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
+base_score.cpp      fragment.o            rddrive.h             score_ph4.o
+base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
+base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
+conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
+conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
+conf_gen_ag.o       grid.h                README                score_solvent.h
+conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
+conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
+conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
+conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
+conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
+conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
+conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
+conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
+conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
+conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
+conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
+conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
+conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
+conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
+conf_gen_hdb.o      lol                   score_footprint.h     trace.o
+defreal.h           Makefile              score_footprint.o     utils.cpp
+dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
+dockmol.cpp         master_conf.h         score_gist.h          utils.o
+dockmol.h           master_conf.o         score_gist.o          version.h
+dockmol.o           master_score.cpp      score.h               xlogp.cpp
+dock.o              master_score.h        score_hbond.cpp       xlogp.h
+filter.cpp          master_score.o        score_hbond.h
+filter.h            mem_info.cpp          score_hbond.o
+(base) [ehspector@login1 dock]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    ../../install/test/minimization/minimize7.dockout
+	modified:   dock.cpp
+	modified:   filter.cpp
+	modified:   filter.h
+	modified:   orient.cpp
+	modified:   ../rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	lol
+	../rdkit/boost/
+	../rdkit/boost_1_71_0.tar.gz
+	../rdkit/boost_1_71_0/
+	../rdkit/eigen-3.3.9.tar.gz
+	../rdkit/eigen-3.3.9/
+	../rdkit/rdkit-Release_2019_09_1.tar.gz
+	../rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@login1 dock]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_500 % pip install pandas --upgrade
+Requirement already satisfied: pandas in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (2.0.3)
+Collecting pandas
+  Obtaining dependency information for pandas from https://files.pythonhosted.org/packages/a8/44/d9502bf0ed197ba9bf1103c9867d5904ddcaf869e52329787fc54ed70cc8/pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (89 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.9/89.9 kB 1.2 MB/s eta 0:00:00
+Requirement already satisfied: numpy>=1.23.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (1.26.4)
+Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2.8.2)
+Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2023.3.post1)
+Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2023.3)
+Requirement already satisfied: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)
+Downloading pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl (12.6 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.6/12.6 MB 18.7 MB/s eta 0:00:00
+Installing collected packages: pandas
+  Attempting uninstall: pandas
+    Found existing installation: pandas 2.0.3
+    Uninstalling pandas-2.0.3:
+      Successfully uninstalled pandas-2.0.3
+Successfully installed pandas-2.2.3
+(base) supremestudier@Evans-MBP AMS_500 % polaris login
+/Users/supremestudier/anaconda3/lib/python3.11/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
+  from pandas.core import (
+[2025-02-02 22:02:58] INFO     You are successfully logged in to the Polaris   client.py:252
+                               Hub.
+(base) supremestudier@Evans-MBP AMS_500 % python --version
+Python 3.11.5
+(base) supremestudier@Evans-MBP AMS_500 % pip install fsspec==2024.12.0
+Collecting fsspec==2024.12.0
+  Obtaining dependency information for fsspec==2024.12.0 from https://files.pythonhosted.org/packages/de/86/5486b0188d08aa643e127774a99bac51ffa6cf343e3deb0583956dca5b22/fsspec-2024.12.0-py3-none-any.whl.metadata
+  Downloading fsspec-2024.12.0-py3-none-any.whl.metadata (11 kB)
+Downloading fsspec-2024.12.0-py3-none-any.whl (183 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 183.9/183.9 kB 2.5 MB/s eta 0:00:00
+Installing collected packages: fsspec
+  Attempting uninstall: fsspec
+    Found existing installation: fsspec 2023.4.0
+    Uninstalling fsspec-2023.4.0:
+      Successfully uninstalled fsspec-2023.4.0
+ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
+s3fs 2023.4.0 requires fsspec==2023.4.0, but you have fsspec 2024.12.0 which is incompatible.
+Successfully installed fsspec-2024.12.0
+(base) supremestudier@Evans-MBP AMS_500 % conda activate
+(base) supremestudier@Evans-MBP AMS_500 % ls
+Materials	Week_2
+(base) supremestudier@Evans-MBP AMS_500 % conda environment
+usage: conda [-h] [--no-plugins] [-V] COMMAND ...
+conda: error: argument COMMAND: invalid choice: 'environment' (choose from 'clean', 'compare', 'config', 'create', 'info', 'init', 'install', 'list', 'notices', 'package', 'remove', 'uninstall', 'rename', 'run', 'search', 'update', 'upgrade', 'build', 'content-trust', 'convert', 'debug', 'develop', 'doctor', 'index', 'inspect', 'metapackage', 'render', 'skeleton', 'env', 'token', 'pack', 'repo', 'server', 'verify')
+(base) supremestudier@Evans-MBP AMS_500 % conda install fsspec==2024.12.0
+Retrieving notices: ...working... done
+Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
+done
+Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
+Solving environment: done
+==> WARNING: A newer version of conda exists. <==
+  current version: 23.7.4
+  latest version: 25.1.1
+Please update conda by running
+    $ conda update -n base -c defaults conda
+Or to minimize the number of packages updated during conda update use
+     conda install conda=25.1.1
+Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
+WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
+WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
+done
+Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
+Solving environment: - failed
+CondaError: KeyboardInterrupt
+(base) supremestudier@Evans-MBP AMS_500 % cd ..
+(base) supremestudier@Evans-MBP Spring_25 % pip show fsspec
+Name: fsspec
+Version: 2024.12.0
+Summary: File-system specification
+Home-page:
+Author:
+Author-email:
+License: BSD 3-Clause License
+Copyright (c) 2018, Martin Durant
+All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Location: /Users/supremestudier/anaconda3/lib/python3.11/site-packages
+Requires:
+Required-by: dask, datamol, datasets, huggingface-hub, intake, polaris-lib, s3fs
+(base) supremestudier@Evans-MBP Spring_25 % polaris login
+/Users/supremestudier/anaconda3/lib/python3.11/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
+  from pandas.core import (
+[2025-02-03 15:53:30] INFO     You are successfully logged in to the Polaris   client.py:252
+                               Hub.
+(base) supremestudier@Evans-MBP Spring_25 % pip install pymol
+ERROR: Could not find a version that satisfies the requirement pymol (from versions: none)
+ERROR: No matching distribution found for pymol
+(base) supremestudier@Evans-MBP Spring_25 % conda activate
+(base) supremestudier@Evans-MBP Spring_25 % conda install -c schrodinger pymol
+Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
+done
+Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
+CondaError: KeyboardInterrupt
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@login1 ~]$ cd AMS_536/
+(base) [ehspector@login1 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@login1 AMS_536]$ cd class_work/
+(base) [ehspector@login1 class_work]$ ls
+Notes.txt
+(base) [ehspector@login1 class_work]$ vi Notes.txt
+(base) [ehspector@login1 class_work]$ touch commands.txt
+(base) [ehspector@login1 class_work]$ vi commands.txt
+(base) [ehspector@login1 class_work]$ bash commands.txt
+(base) [ehspector@login1 class_work]$ ls
+_structure  commands.txt  Notes.txt
+(base) [ehspector@login1 class_work]$ vi commands.txt
+(base) [ehspector@login1 class_work]$ bash commands.txt
+mkdir: cannot create directory ‘001_structure’: File exists
+(base) [ehspector@login1 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@login1 class_work]$ exit
+logout
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ class
+(base) [ehspector@login1 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@login1 AMS_536]$ cd class_work/
+(base) [ehspector@login1 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@login1 class_work]$ cd 001_structure/
+(base) [ehspector@login1 001_structure]$ pwd
+/gpfs/home/ehspector/AMS_536/class_work/001_structure
+(base) [ehspector@login1 001_structure]$ ^C
+(base) [ehspector@login1 001_structure]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ exit
+logout
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login1 ~]$ class
+(base) [ehspector@login1 AMS_536]$ cd class_work/
+(base) [ehspector@login1 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@login1 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@login1 002_surface_spheres]$ ls
+w26_surface.dms
+(base) [ehspector@login1 002_surface_spheres]$ vi INSPH
+(base) [ehspector@login1 002_surface_spheres]$ vi INSPH
+(base) [ehspector@login1 002_surface_spheres]$ sphgen -i INSPH -o OUTSPH
+bash: sphgen: command not found...
+(base) [ehspector@login1 002_surface_spheres]$ which sphgen
+/usr/bin/which: no sphgen in (/gpfs/home/ehspector/miniconda3/bin:/gpfs/home/ehspector/miniconda3/condabin:/gpfs/software/mvapich/haswell/gcc13.2/2.3.7/bin:/gpfs/software/gcc/haswell/13.2.0/bin:/cm/shared/apps/slurm/17.11.12/sbin:/cm/shared/apps/slurm/17.11.12/bin:/cm/local/apps/environment-modules/4.0.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/4.0.0/bin:/gpfs/software/local/bin:/gpfs/projects/rizzo/espector/builds/alpha_branch/bin:/gpfs/home/ehspector/bin)
+(base) [ehspector@login1 002_surface_spheres]$ cd ..
+(base) [ehspector@login1 class_work]$ cd ..
+(base) [ehspector@login1 AMS_536]$ cd ..
+(base) [ehspector@login1 ~]$ cd ..
+(base) [ehspector@login1 home]$ cd ..
+(base) [ehspector@login1 gpfs]$ cd projects/AMS536
+(base) [ehspector@login1 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@login1 AMS536]$ cd 2025/
+(base) [ehspector@login1 2025]$ ls
+additional_files  robbashrc_file  rotations  wed_humpday.txt
+(base) [ehspector@login1 2025]$ cd ..
+(base) [ehspector@login1 AMS536]$ cd zzz.programs/
+(base) [ehspector@login1 zzz.programs]$ ls
+amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
+de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
+dock6.10         dock6.12         gen-frags-12         VS_libraries
+dock6.10_milan   dock6.12_ams536  old
+(base) [ehspector@login1 zzz.programs]$ cd dock6.12_ams536
+(base) [ehspector@login1 dock6.12_ams536]$ ls
+bin  developer  docs  install  parameters  README  README.md  src  template_pipeline  tutorials
+(base) [ehspector@login1 dock6.12_ams536]$ cd bin/
+(base) [ehspector@login1 bin]$ ls
+am1bcc             combine_torenv.py  mol2bild.py          parmchk               showsphere
+amberize_complex   dock6              mol2.py              prepare_amber.pl      solvgrid
+amberize_ligand    dock6.mpi          mopac                prepare_rna_amber.pl  solvmap
+amberize_receptor  espgen             mopac.sh             prepgen               sphere_selector
+antechamber        grid               multigrid_fp_gen.py  resp                  sphgen
+atomtype           grid-convert       nchemgrid_GB         respgen               teLeap
+bondtype           grid-convrds       nchemgrid_SA         sevsolv               tleap
+chemgrid           make_phimap        parmcal              showbox
+(base) [ehspector@login1 bin]$ pwd
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
+(base) [ehspector@login1 bin]$ class
+(base) [ehspector@login1 AMS_536]$ cd class_work/
+(base) [ehspector@login1 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@login1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen)
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
+(base) [ehspector@login1 002_surface_spheres]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd class_work/
+(base) [ehspector@milan1 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+w26_surface.dms  INSPH
+(base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
+At line 328 of file sphgen.f
+Fortran runtime error: Bad value during floating point read
+Error termination. Backtrace:
+#0  0x7ffff7d59e39 in formatted_transfer_scalar_read
+	at ../../../libgfortran/io/transfer.c:1790
+#1  0x7ffff7d5b535 in formatted_transfer
+	at ../../../libgfortran/io/transfer.c:2491
+#2  0x4049e0 in ???
+#3  0x40516a in ???
+#4  0x40117c in ???
+#5  0x7ffff742958f in ???
+#6  0x7ffff742963f in ???
+#7  0x4011b4 in ???
+#8  0xffffffffffffffff in ???
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+w26_surface.dms  INSPH  OUTSPH  temp1.ms  temp3.atc
+(base) [ehspector@milan1 002_surface_spheres]$ rm 2w26_surface.dms
+(base) [ehspector@milan1 002_surface_spheres]$ rm temp1.ms temp3.atc
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+INSPH  OUTSPH
+(base) [ehspector@milan1 002_surface_spheres]$ rm OUTSPH
+(base) [ehspector@milan1 002_surface_spheres]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd class_work
+(base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+w26_new_surface.dms  INSPH
+(base) [ehspector@milan1 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH
+(base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH
+(base) [ehspector@milan1 002_surface_spheres]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ module load git
+(base) [ehspector@milan2 ~]$ home
+(base) [ehspector@milan2 espector]$ cd builds/
+(base) [ehspector@milan2 builds]$ cd alpha_branch/
+(base) [ehspector@milan2 alpha_branch]$ git branch
+* alpha_branch
+  master
+(base) [ehspector@milan2 alpha_branch]$ git pull
+/gpfs/software/git/2.36.2/libexec/git-core/git-remote-https: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory
+(base) [ehspector@milan2 alpha_branch]$ module list
+Currently Loaded Modulefiles:
+) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack
+) shared                   4) mvapich2/gcc13.2/2.3.7   6) git/2.36.2
+(base) [ehspector@milan2 alpha_branch]$ module unload git
+(base) [ehspector@milan2 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+Updating 4be5c842..2ce698b4
+error: Your local changes to the following files would be overwritten by merge:
+	src/dock/dock.cpp
+	src/dock/orient.cpp
+Please commit your changes or stash them before you merge.
+Aborting
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+  (use "git pull" to update your local branch)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+	modified:   src/dock/dock.cpp
+	modified:   src/dock/filter.cpp
+	modified:   src/dock/filter.h
+	modified:   src/dock/orient.cpp
+	modified:   src/rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@milan2 alpha_branch]$ git add
+Nothing specified, nothing added.
+hint: Maybe you wanted to say 'git add .'?
+hint: Turn this message off by running
+hint: "git config advice.addEmptyPathspec false"
+(base) [ehspector@milan2 alpha_branch]$ git add src/dock/dock.cpp src/dock/filter.cpp src/dock/filter.h
+(base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: ability to gasterize mols"
+[alpha_branch 8c38cd54] feat: ability to gasterize mols
+files changed, 70 insertions(+), 8 deletions(-)
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch and 'origin/alpha_branch' have diverged,
+and have 1 and 267 different commits each, respectively.
+  (use "git pull" if you want to integrate the remote branch with yours)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+	modified:   src/dock/orient.cpp
+	modified:   src/rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@milan2 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+hint: You have divergent branches and need to specify how to reconcile them.
+hint: You can do so by running one of the following commands sometime before
+hint: your next pull:
+hint:
+hint:   git config pull.rebase false  # merge
+hint:   git config pull.rebase true   # rebase
+hint:   git config pull.ff only       # fast-forward only
+hint:
+hint: You can replace "git config" with "git config --global" to set a default
+hint: preference for all repositories. You can also pass --rebase, --no-rebase,
+hint: or --ff-only on the command line to override the configured default per
+hint: invocation.
+fatal: Need to specify how to reconcile divergent branches.
+(base) [ehspector@milan2 alpha_branch]$ git pull --rebase
+error: cannot pull with rebase: You have unstaged changes.
+error: Please commit or stash them.
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch and 'origin/alpha_branch' have diverged,
+and have 1 and 267 different commits each, respectively.
+  (use "git pull" if you want to integrate the remote branch with yours)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+	modified:   src/dock/orient.cpp
+	modified:   src/rdkit/Makefile
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@milan2 alpha_branch]$ git add  src/dock/orient.cpp
+(base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: shows number of spheres generated"
+[alpha_branch 704ff10f] feat: shows number of spheres generated
+file changed, 3 insertions(+), 3 deletions(-)
+(base) [ehspector@milan2 alpha_branch]$ git add src/rdkit/Makefile
+(base) [ehspector@milan2 alpha_branch]$ git commit -m "fix: replaces boost url with working one "
+[alpha_branch 123e4913] fix: replaces boost url with working one
+file changed, 3 insertions(+), 1 deletion(-)
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch and 'origin/alpha_branch' have diverged,
+and have 3 and 267 different commits each, respectively.
+  (use "git pull" if you want to integrate the remote branch with yours)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@milan2 alpha_branch]$ git push
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+remote: Support for password authentication was removed on August 13, 2021.
+remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
+fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
+(base) [ehspector@milan2 alpha_branch]$ git push
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+To https://github.com/EvanS-Dock6/dock6.git
+ ! [rejected]          alpha_branch -> alpha_branch (non-fast-forward)
+error: failed to push some refs to 'https://github.com/EvanS-Dock6/dock6.git'
+hint: Updates were rejected because the tip of your current branch is behind
+hint: its remote counterpart. If you want to integrate the remote changes,
+hint: use 'git pull' before pushing again.
+hint: See the 'Note about fast-forwards' in 'git push --help' for details.
+(base) [ehspector@milan2 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+hint: You have divergent branches and need to specify how to reconcile them.
+hint: You can do so by running one of the following commands sometime before
+hint: your next pull:
+hint:
+hint:   git config pull.rebase false  # merge
+hint:   git config pull.rebase true   # rebase
+hint:   git config pull.ff only       # fast-forward only
+hint:
+hint: You can replace "git config" with "git config --global" to set a default
+hint: preference for all repositories. You can also pass --rebase, --no-rebase,
+hint: or --ff-only on the command line to override the configured default per
+hint: invocation.
+fatal: Need to specify how to reconcile divergent branches.
+(base) [ehspector@milan2 alpha_branch]$ git pull --rebase
+error: cannot pull with rebase: You have unstaged changes.
+error: Please commit or stash them.
+(base) [ehspector@milan2 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch and 'origin/alpha_branch' have diverged,
+and have 3 and 267 different commits each, respectively.
+  (use "git pull" if you want to integrate the remote branch with yours)
+Changes not staged for commit:
+  (use "git add/rm <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	deleted:    install/test/minimization/minimize7.dockout
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@milan2 alpha_branch]$ git rm install/test/minimization/minimize7.dockout
+rm 'install/test/minimization/minimize7.dockout'
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch and 'origin/alpha_branch' have diverged,
+and have 3 and 267 different commits each, respectively.
+  (use "git pull" if you want to integrate the remote branch with yours)
+Changes to be committed:
+  (use "git restore --staged <file>..." to unstage)
+	deleted:    install/test/minimization/minimize7.dockout
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+(base) [ehspector@milan2 alpha_branch]$ git commit -m "build: rm minimize.docot"
+[alpha_branch fe018e1e] build: rm minimize.docot
+file changed, 187 deletions(-)
+ delete mode 100644 install/test/minimization/minimize7.dockout
+(base) [ehspector@milan2 alpha_branch]$ git push
+Username for 'https://github.com': ^C
+(base) [ehspector@milan2 alpha_branch]$ git pull
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+hint: You have divergent branches and need to specify how to reconcile them.
+hint: You can do so by running one of the following commands sometime before
+hint: your next pull:
+hint:
+hint:   git config pull.rebase false  # merge
+hint:   git config pull.rebase true   # rebase
+hint:   git config pull.ff only       # fast-forward only
+hint:
+hint: You can replace "git config" with "git config --global" to set a default
+hint: preference for all repositories. You can also pass --rebase, --no-rebase,
+hint: or --ff-only on the command line to override the configured default per
+hint: invocation.
+fatal: Need to specify how to reconcile divergent branches.
+(base) [ehspector@milan2 alpha_branch]$ git pull --rebase
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+Successfully rebased and updated refs/heads/alpha_branch.
+(base) [ehspector@milan2 alpha_branch]$ git status
+On branch alpha_branch
+Your branch is ahead of 'origin/alpha_branch' by 4 commits.
+  (use "git push" to publish your local commits)
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+nothing added to commit but untracked files present (use "git add" to track)
+(base) [ehspector@milan2 alpha_branch]$ git push
+Username for 'https://github.com': EvanS-Dock6
+Password for 'https://EvanS-Dock6@github.com':
+Enumerating objects: 34, done.
+Counting objects: 100% (34/34), done.
+Delta compression using up to 128 threads
+Compressing objects: 100% (21/21), done.
+Writing objects: 100% (22/22), 2.96 KiB | 2.96 MiB/s, done.
+Total 22 (delta 17), reused 0 (delta 0), pack-reused 0
+remote: Resolving deltas: 100% (17/17), completed with 11 local objects.
+To https://github.com/EvanS-Dock6/dock6.git
+ce698b4..5f99310b  alpha_branch -> alpha_branch
+(base) [ehspector@milan2 alpha_branch]$ docs
+-bash: docs: command not found
+(base) [ehspector@milan2 alpha_branch]$ cd docs
+(base) [ehspector@milan2 docs]$ ls
+bugfixes610  bugfixes65    dock6_manual.html  new_in_6.11.txt  new_in_6.4.txt  README
+bugfixes611  bugfixes66    faq                new_in_6.12.txt  new_in_6.5.txt  tutorials
+bugfixes612  bugfixes67    faq.htm            new_in_6.13.txt  new_in_6.6.txt
+bugfixes62   bugfixes68    images             new_in_6.1.txt   new_in_6.7.txt
+bugfixes63   bugfixes69    index.htm          new_in_6.2.txt   new_in_6.8.txt
+bugfixes64   bugfixes.htm  new_in_6.10.txt    new_in_6.3.txt   new_in_6.9.txt
+(base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
+(base) [ehspector@milan2 docs]$ home
+(base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@milan2 gas_teiger]$ vi gas.in
+(base) [ehspector@milan2 gas_teiger]$ home
+(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs
+(base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
+(base) [ehspector@milan2 docs]$ vi dock6_manual.html
+(base) [ehspector@milan2 docs]$ pwd
+/gpfs/projects/rizzo/espector/builds/alpha_branch/docs
+(base) [ehspector@milan2 docs]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ home
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ cd ..
+(base) [ehspector@milan2 rizzo]$ class
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@milan2 AMS_536]$ cd class_work/
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
+w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi 2w26.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphere_selector 2w26.sph ../001_structure/2w26_ligand_hydrogens_charges.mol2 10.0
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 003
+-bash: cd: 003: No such file or directory
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 002
+-bash: cd: 002: No such file or directory
+(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh  showbox.in
+(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
+ automatically construct box to enclose spheres [Y/N]?
+ extra margin to also be enclosed (angstroms)?
+   (this will be added in all 6 directions)
+ sphere file-
+ cluster number-
+At line 61 of file showbox.f (unit = 1)
+Fortran runtime error: Cannot open file '../002_spheres/selected_spheres.sph': No such file or directory
+Error termination. Backtrace:
+#0  0x7ffff7d54ca5 in already_open
+	at ../../../libgfortran/io/open.c:742
+#1  0x4015d9 in ???
+#2  0x40115c in ???
+#3  0x7ffff742958f in ???
+#4  0x7ffff742963f in ???
+#5  0x401194 in ???
+#6  0xffffffffffffffff in ???
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh  showbox.in
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 003
+-bash: cd: 003: No such file or directory
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh  showbox.in
+(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
+showbox.sh: line 3: syntax error near unexpected token `&'
+showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < &showbox.in&'
+(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
+showbox.sh: line 3: syntax error near unexpected token `&'
+showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < showbox.in > &showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi 2w26.box.pdb
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ tar -cvf 2w26
+tar: Cowardly refusing to create an empty archive
+Try 'tar --help' or 'tar --usage' for more information.
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  class_work
+(base) [ehspector@milan2 AMS_536]$ cd class_
+-bash: cd: class_: No such file or directory
+(base) [ehspector@milan2 AMS_536]$ cd class_work/
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
+w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi grid.
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi grid.out
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi grid.out
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
+w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
+(base) [ehspector@milan2 001_structure]$ vi 2w26_protein_with_charges.mol2
+(base) [ehspector@milan2 001_structure]$ pwd
+/gpfs/home/ehspector/AMS_536/class_work/001_structure
+(base) [ehspector@milan2 001_structure]$ homw
+-bash: homw: command not found
+(base) [ehspector@milan2 001_structure]$ home
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ cd gas_test/
+(base) [ehspector@milan2 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@milan2 gas_test]$ cd ..
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ cd gas_test/
+(base) [ehspector@milan2 gas_test]$ vi test.in
+(base) [ehspector@milan2 gas_test]$ vi test_2.in
+(base) [ehspector@milan2 gas_test]$ cd gas_f_test/
+(base) [ehspector@milan2 gas_f_test]$ ls
+diff.out   gas_0.out_scored.mol2  gas_1.out              gas_50.in   gas_50.out_scored.mol2
+gas_0.out  gas_1.in               gas_1.out_scored.mol2  gas_50.out
+(base) [ehspector@milan2 gas_f_test]$ vi gas_1.in
+(base) [ehspector@milan2 gas_f_test]$ cd ..
+(base) [ehspector@milan2 gas_test]$ cd ..
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ cd gas_test/
+(base) [ehspector@milan2 gas_test]$ ls
+s0v_GA.in                       4s0v_GA_output.restart0028.mol2
+s0v_GA.out                      4s0v_GA_output.restart0029.mol2
+s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
+s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
+s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
+s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
+s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
+s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
+s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
+s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
+s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
+s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
+s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
+s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
+s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
+s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
+s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
+s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
+s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
+s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
+s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
+s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
+s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
+s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
+s0v_GA_output.restart0022.mol2  charge_data
+s0v_GA_output.restart0023.mol2  gas_f_test
+s0v_GA_output.restart0024.mol2  gas_RD_Test
+s0v_GA_output.restart0025.mol2  GA.txt
+s0v_GA_output.restart0026.mol2  test_2.in
+s0v_GA_output.restart0027.mol2  test.in
+(base) [ehspector@milan2 gas_test]$ cd gas_f_test/
+(base) [ehspector@milan2 gas_f_test]$ ls
+diff.out   gas_0.out_scored.mol2  gas_1.out              gas_50.in   gas_50.out_scored.mol2
+gas_0.out  gas_1.in               gas_1.out_scored.mol2  gas_50.out
+(base) [ehspector@milan2 gas_f_test]$ cp gas_1.in gas_2.in
+(base) [ehspector@milan2 gas_f_test]$ vi gas_2.in
+(base) [ehspector@milan2 gas_f_test]$ vi gas_2.in
+(base) [ehspector@milan2 gas_f_test]$ dock6 -i gas_2.in -o gas_2.out
+^C
+(base) [ehspector@milan2 gas_f_test]$ ls
+diff.out               gas_1.in               gas_2.in   gas_50.out
+gas_0.out              gas_1.out              gas_2.out  gas_50.out_scored.mol2
+gas_0.out_scored.mol2  gas_1.out_scored.mol2  gas_50.in  gas.out_scored.mol2
+(base) [ehspector@milan2 gas_f_test]$ vi gas_2.out
+(base) [ehspector@milan2 gas_f_test]$ home
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs/
+(base) [ehspector@milan2 docs]$ ls
+bugfixes610  bugfixes65    dock6_manual.html  new_in_6.11.txt  new_in_6.4.txt  README
+bugfixes611  bugfixes66    faq                new_in_6.12.txt  new_in_6.5.txt  tutorials
+bugfixes612  bugfixes67    faq.htm            new_in_6.13.txt  new_in_6.6.txt
+bugfixes62   bugfixes68    images             new_in_6.1.txt   new_in_6.7.txt
+bugfixes63   bugfixes69    index.htm          new_in_6.2.txt   new_in_6.8.txt
+bugfixes64   bugfixes.htm  new_in_6.10.txt    new_in_6.3.txt   new_in_6.9.txt
+(base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
+(base) [ehspector@milan2 docs]$ class
+(base) [ehspector@milan2 AMS_536]$ mkdir 1086 5EEN
+(base) [ehspector@milan2 AMS_536]$ ls
+  5EEN  class_project  class_work
+(base) [ehspector@milan2 AMS_536]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Spring_25 % cd AMS_536/Tutorial
+(base) supremestudier@Evans-MBP Tutorial % ls
+w26.box.pdb
+w26.pdb
+w26.pdb1.gz
+w26.sph
+w26_charges.pdb
+w26_ligand.pdb
+w26_ligand_hydrogens_charges.mol2
+w26_ligand_hydrogens_charges.pdb
+w26_ligand_no_hydrogens_no_charges.mol2
+w26_new_surface.dms
+w26_protein_no_hydrogens_no_charges.mol2
+w26_protein_only.pdb
+w26_protein_with_charges.mol2
+w26_surface.dms
+selected_spheres.sph
+(base) supremestudier@Evans-MBP Tutorial % vi 2w26.pdb
+(base) supremestudier@Evans-MBP Tutorial % ls
+w26.box.pdb
+w26.pdb
+w26.pdb1.gz
+w26.sph
+w26_charges.pdb
+w26_ligand.pdb
+w26_ligand_hydrogens_charges.mol2
+w26_ligand_hydrogens_charges.pdb
+w26_ligand_no_hydrogens_no_charges.mol2
+w26_new_surface.dms
+w26_protein_no_hydrogens_no_charges.mol2
+w26_protein_only.pdb
+w26_protein_with_charges.mol2
+w26_surface.dms
+selected_spheres.sph
+(base) supremestudier@Evans-MBP Tutorial % mdkir 2w26
+zsh: command not found: mdkir
+(base) supremestudier@Evans-MBP Tutorial % mkdir 2w26
+(base) supremestudier@Evans-MBP Tutorial % ls
+w26
+w26.box.pdb
+w26.pdb
+w26.pdb1.gz
+w26.sph
+w26_charges.pdb
+w26_ligand.pdb
+w26_ligand_hydrogens_charges.mol2
+w26_ligand_hydrogens_charges.pdb
+w26_ligand_no_hydrogens_no_charges.mol2
+w26_new_surface.dms
+w26_protein_no_hydrogens_no_charges.mol2
+w26_protein_only.pdb
+w26_protein_with_charges.mol2
+w26_surface.dms
+selected_spheres.sph
+(base) supremestudier@Evans-MBP Tutorial % cd ..
+(base) supremestudier@Evans-MBP AMS_536 % cd ..
+(base) supremestudier@Evans-MBP Spring_25 % cd AMS_548
+(base) supremestudier@Evans-MBP AMS_548 % ls
+Polaris.ipynb				ligand_poses_reference_structures.zip
+ligand_poses_reference_structures
+(base) supremestudier@Evans-MBP AMS_548 % pwd
+/Users/supremestudier/Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_548
+(base) supremestudier@Evans-MBP AMS_548 % pip install pymol
+ERROR: Could not find a version that satisfies the requirement pymol (from versions: none)
+ERROR: No matching distribution found for pymol
+(base) supremestudier@Evans-MBP AMS_548 % which python
+/Users/supremestudier/anaconda3/bin/python
+(base) supremestudier@Evans-MBP AMS_548 % tar -jxf pymol-X_XX-bin-linux-x86-glibc23.tar.bz2
+tar: Error opening archive: Failed to open 'pymol-X_XX-bin-linux-x86-glibc23.tar.bz2'
+(base) supremestudier@Evans-MBP AMS_548 % conda install -c conda-forge -c schrodinger pymol-bundle
+Retrieving notices: ...working... done
+Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
+done
+Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
+Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
+Collecting package metadata (repodata.json): / WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
+WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
+WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
+done
+Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
+CondaError: KeyboardInterrupt
+(base) supremestudier@Evans-MBP AMS_548 %
+(base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U
+Collecting boltz
+  Obtaining dependency information for boltz from https://files.pythonhosted.org/packages/22/b3/6bbc7aaea024d3dc13abc8e94ee32df74dd63bfc016e0f87abd20d0dcbbd/boltz-0.4.1-py3-none-any.whl.metadata
+  Downloading boltz-0.4.1-py3-none-any.whl.metadata (4.8 kB)
+Collecting torch>=2.2 (from boltz)
+  Obtaining dependency information for torch>=2.2 from https://files.pythonhosted.org/packages/3f/14/e105b8ef6d324e789c1589e95cb0ab63f3e07c2216d68b1178b7c21b7d2a/torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl.metadata
+  Downloading torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl.metadata (25 kB)
+Collecting numpy==1.26.3 (from boltz)
+  Obtaining dependency information for numpy==1.26.3 from https://files.pythonhosted.org/packages/42/db/82cc805d96ba48622fbb7395a7b44cf59567fca235e397cdf64555081773/numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (61 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 1.2 MB/s eta 0:00:00
+Collecting hydra-core==1.3.2 (from boltz)
+  Obtaining dependency information for hydra-core==1.3.2 from https://files.pythonhosted.org/packages/c6/50/e0edd38dcd63fb26a8547f13d28f7a008bc4a3fd4eb4ff030673f22ad41a/hydra_core-1.3.2-py3-none-any.whl.metadata
+  Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
+Collecting pytorch-lightning==2.4.0 (from boltz)
+  Obtaining dependency information for pytorch-lightning==2.4.0 from https://files.pythonhosted.org/packages/2b/d2/ecd65ff1e0b1ca79f9785dd65d5ced7ec2643a828068aaa24e47e4c84a14/pytorch_lightning-2.4.0-py3-none-any.whl.metadata
+  Downloading pytorch_lightning-2.4.0-py3-none-any.whl.metadata (21 kB)
+Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
+Collecting dm-tree==0.1.8 (from boltz)
+  Obtaining dependency information for dm-tree==0.1.8 from https://files.pythonhosted.org/packages/b1/65/4f10a68dde5fa0c91043c9c899e9bc79b1657ba932d39a5f8525c0058e68/dm_tree-0.1.8-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading dm_tree-0.1.8-cp311-cp311-macosx_10_9_x86_64.whl.metadata (1.9 kB)
+Collecting requests==2.32.3 (from boltz)
+  Obtaining dependency information for requests==2.32.3 from https://files.pythonhosted.org/packages/f9/9b/335f9764261e915ed497fcdeb11df5dfd6f7bf257d4a6a2a686d80da4d54/requests-2.32.3-py3-none-any.whl.metadata
+  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
+Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
+Collecting types-requests (from boltz)
+  Obtaining dependency information for types-requests from https://files.pythonhosted.org/packages/d7/01/485b3026ff90e5190b5e24f1711522e06c79f4a56c8f4b95848ac072e20f/types_requests-2.32.0.20241016-py3-none-any.whl.metadata
+  Downloading types_requests-2.32.0.20241016-py3-none-any.whl.metadata (1.9 kB)
+Collecting einops==0.8.0 (from boltz)
+  Obtaining dependency information for einops==0.8.0 from https://files.pythonhosted.org/packages/44/5a/f0b9ad6c0a9017e62d4735daaeb11ba3b6c009d69a26141b258cd37b5588/einops-0.8.0-py3-none-any.whl.metadata
+  Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
+Collecting einx==0.3.0 (from boltz)
+  Obtaining dependency information for einx==0.3.0 from https://files.pythonhosted.org/packages/90/04/4a730d74fd908daad86d6b313f235cdf8e0cf1c255b392b7174ff63ea81a/einx-0.3.0-py3-none-any.whl.metadata
+  Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)
+Collecting fairscale==0.4.13 (from boltz)
+  Downloading fairscale-0.4.13.tar.gz (266 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 266.3/266.3 kB 4.7 MB/s eta 0:00:00
+  Installing build dependencies ... done
+  Getting requirements to build wheel ... done
+  Installing backend dependencies ... done
+  Preparing metadata (pyproject.toml) ... done
+Collecting mashumaro==3.14 (from boltz)
+  Obtaining dependency information for mashumaro==3.14 from https://files.pythonhosted.org/packages/1b/35/8d63733a2c12149d0c7663c29bf626bdbeea5f0ff963afe58a42b4810981/mashumaro-3.14-py3-none-any.whl.metadata
+  Downloading mashumaro-3.14-py3-none-any.whl.metadata (114 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 114.4/114.4 kB 3.3 MB/s eta 0:00:00
+Collecting modelcif==1.2 (from boltz)
+  Downloading modelcif-1.2.tar.gz (66 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 2.3 MB/s eta 0:00:00
+  Preparing metadata (setup.py) ... done
+Collecting wandb==0.18.7 (from boltz)
+  Obtaining dependency information for wandb==0.18.7 from https://files.pythonhosted.org/packages/0c/6d/cf600f649090d3c3f8ac86becf10a1d3d5c1ce305389c4d02cc9488fb8d0/wandb-0.18.7-py3-none-macosx_10_13_x86_64.whl.metadata
+  Downloading wandb-0.18.7-py3-none-macosx_10_13_x86_64.whl.metadata (9.7 kB)
+Collecting click==8.1.7 (from boltz)
+  Obtaining dependency information for click==8.1.7 from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata
+  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
+Collecting pyyaml==6.0.2 (from boltz)
+  Obtaining dependency information for pyyaml==6.0.2 from https://files.pythonhosted.org/packages/f8/aa/7af4e81f7acba21a4c6be026da38fd2b872ca46226673c89a758ebdc4fd2/PyYAML-6.0.2-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading PyYAML-6.0.2-cp311-cp311-macosx_10_9_x86_64.whl.metadata (2.1 kB)
+Collecting biopython==1.84 (from boltz)
+  Obtaining dependency information for biopython==1.84 from https://files.pythonhosted.org/packages/c5/7b/c1e9f66e23b01958ae0284a437a0e586ce20387fc6ea0382c21230ac59bc/biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl.metadata (12 kB)
+Collecting scipy==1.13.1 (from boltz)
+  Obtaining dependency information for scipy==1.13.1 from https://files.pythonhosted.org/packages/b4/15/4a4bb1b15bbd2cd2786c4f46e76b871b28799b67891f23f455323a0cdcfb/scipy-1.13.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata
+  Downloading scipy-1.13.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata (60 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 1.9 MB/s eta 0:00:00
+Requirement already satisfied: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (1.11.1)
+Collecting frozendict (from einx==0.3.0->boltz)
+  Obtaining dependency information for frozendict from https://files.pythonhosted.org/packages/04/13/d9839089b900fa7b479cce495d62110cddc4bd5630a04d8469916c0e79c5/frozendict-2.4.6-py311-none-any.whl.metadata
+  Downloading frozendict-2.4.6-py311-none-any.whl.metadata (23 kB)
+Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz)
+  Obtaining dependency information for omegaconf<2.4,>=2.2 from https://files.pythonhosted.org/packages/e3/94/1843518e420fa3ed6919835845df698c7e27e183cb997394e4a670973a65/omegaconf-2.3.0-py3-none-any.whl.metadata
+  Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)
+Collecting antlr4-python3-runtime==4.9.* (from hydra-core==1.3.2->boltz)
+  Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.0/117.0 kB 3.4 MB/s eta 0:00:00
+  Preparing metadata (setup.py) ... done
+Requirement already satisfied: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
+Requirement already satisfied: typing-extensions>=4.1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from mashumaro==3.14->boltz) (4.12.2)
+Collecting ihm>=1.7 (from modelcif==1.2->boltz)
+  Downloading ihm-1.8.tar.gz (350 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 350.7/350.7 kB 7.3 MB/s eta 0:00:00
+  Preparing metadata (setup.py) ... done
+Requirement already satisfied: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
+Requirement already satisfied: fsspec[http]>=2022.5.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (2024.12.0)
+Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz)
+  Obtaining dependency information for torchmetrics>=0.7.0 from https://files.pythonhosted.org/packages/9d/e1/84066ff60a20dfa63f4d9d8ddc280d5ed323b7f06504dbb51c523b690116/torchmetrics-1.6.1-py3-none-any.whl.metadata
+  Downloading torchmetrics-1.6.1-py3-none-any.whl.metadata (21 kB)
+Collecting lightning-utilities>=0.10.0 (from pytorch-lightning==2.4.0->boltz)
+  Obtaining dependency information for lightning-utilities>=0.10.0 from https://files.pythonhosted.org/packages/50/8d/da77ceb92ed674da93959184a2777d08ccbd872559fb52aba16b91686b7e/lightning_utilities-0.12.0-py3-none-any.whl.metadata
+  Downloading lightning_utilities-0.12.0-py3-none-any.whl.metadata (5.6 kB)
+Requirement already satisfied: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
+Requirement already satisfied: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
+Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (1.26.16)
+Requirement already satisfied: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
+Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz)
+  Obtaining dependency information for docker-pycreds>=0.4.0 from https://files.pythonhosted.org/packages/f5/e8/f6bd1eee09314e7e6dee49cbe2c5e22314ccdb38db16c9fc72d2fa80d054/docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata
+  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB)
+Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz)
+  Obtaining dependency information for gitpython!=3.1.29,>=1.0.0 from https://files.pythonhosted.org/packages/1d/9a/4114a9057db2f1462d5c8f8390ab7383925fe1ac012eaa42402ad65c2963/GitPython-3.1.44-py3-none-any.whl.metadata
+  Downloading GitPython-3.1.44-py3-none-any.whl.metadata (13 kB)
+Requirement already satisfied: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
+Requirement already satisfied: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
+Requirement already satisfied: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
+Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz)
+  Obtaining dependency information for sentry-sdk>=2.0.0 from https://files.pythonhosted.org/packages/e6/0f/6f7e6cd0f4a141752caef3f79300148422fdf2b8b68b531f30b2b0c0cbda/sentry_sdk-2.20.0-py2.py3-none-any.whl.metadata
+  Downloading sentry_sdk-2.20.0-py2.py3-none-any.whl.metadata (10 kB)
+Collecting setproctitle (from wandb==0.18.7->boltz)
+  Obtaining dependency information for setproctitle from https://files.pythonhosted.org/packages/5d/1a/1fb7d622195bcb3ce7b04366a833e51cfa5ad632c5dafe32e0763cd3fdc9/setproctitle-1.3.4-cp311-cp311-macosx_10_9_universal2.whl.metadata
+  Downloading setproctitle-1.3.4-cp311-cp311-macosx_10_9_universal2.whl.metadata (10 kB)
+Requirement already satisfied: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
+Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
+Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
+Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
+Requirement already satisfied: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
+Requirement already satisfied: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
+Requirement already satisfied: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
+Requirement already satisfied: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
+Collecting urllib3<3,>=1.21.1 (from requests==2.32.3->boltz)
+  Obtaining dependency information for urllib3<3,>=1.21.1 from https://files.pythonhosted.org/packages/c8/19/4ec628951a74043532ca2cf5d97b7b14863931476d117c471e8e2b1eb39f/urllib3-2.3.0-py3-none-any.whl.metadata
+  Downloading urllib3-2.3.0-py3-none-any.whl.metadata (6.5 kB)
+Requirement already satisfied: six>=1.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz) (1.16.0)
+Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (3.8.5)
+Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz)
+  Obtaining dependency information for gitdb<5,>=4.0.1 from https://files.pythonhosted.org/packages/a0/61/5c78b91c3143ed5c14207f463aecfc8f9dbb5092fb2869baf37c273b2705/gitdb-4.0.12-py3-none-any.whl.metadata
+  Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
+Requirement already satisfied: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
+Requirement already satisfied: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
+Requirement already satisfied: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->einx==0.3.0->boltz) (1.3.0)
+Requirement already satisfied: attrs>=17.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (22.1.0)
+Requirement already satisfied: multidict<7.0,>=4.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (6.0.2)
+Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (4.0.2)
+Requirement already satisfied: yarl<2.0,>=1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.8.1)
+Requirement already satisfied: frozenlist>=1.1.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.3.3)
+Requirement already satisfied: aiosignal>=1.1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.2.0)
+Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz)
+  Obtaining dependency information for smmap<6,>=3.0.1 from https://files.pythonhosted.org/packages/04/be/d09147ad1ec7934636ad912901c5fd7667e1c858e19d355237db0d0cd5e4/smmap-5.0.2-py3-none-any.whl.metadata
+  Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
+Downloading boltz-0.4.1-py3-none-any.whl (138 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 138.5/138.5 kB 4.3 MB/s eta 0:00:00
+Downloading biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl (2.8 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 16.5 MB/s eta 0:00:00
+Downloading click-8.1.7-py3-none-any.whl (97 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 2.8 MB/s eta 0:00:00
+Downloading dm_tree-0.1.8-cp311-cp311-macosx_10_9_x86_64.whl (115 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 115.4/115.4 kB 3.5 MB/s eta 0:00:00
+Downloading einops-0.8.0-py3-none-any.whl (43 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.2/43.2 kB 1.2 MB/s eta 0:00:00
+Downloading einx-0.3.0-py3-none-any.whl (102 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.0/103.0 kB 2.9 MB/s eta 0:00:00
+Downloading hydra_core-1.3.2-py3-none-any.whl (154 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.5/154.5 kB 4.1 MB/s eta 0:00:00
+Downloading mashumaro-3.14-py3-none-any.whl (92 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.2/92.2 kB 2.7 MB/s eta 0:00:00
+Downloading numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl (20.6 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.6/20.6 MB 14.9 MB/s eta 0:00:00
+Downloading pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 815.2/815.2 kB 11.3 MB/s eta 0:00:00
+Downloading PyYAML-6.0.2-cp311-cp311-macosx_10_9_x86_64.whl (184 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 184.6/184.6 kB 4.8 MB/s eta 0:00:00
+Downloading requests-2.32.3-py3-none-any.whl (64 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.9/64.9 kB 2.1 MB/s eta 0:00:00
+Downloading scipy-1.13.1-cp311-cp311-macosx_10_9_x86_64.whl (39.3 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.3/39.3 MB 14.3 MB/s eta 0:00:00
+Downloading wandb-0.18.7-py3-none-macosx_10_13_x86_64.whl (15.8 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.8/15.8 MB 17.7 MB/s eta 0:00:00
+Downloading torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl (150.8 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 150.8/150.8 MB 6.5 MB/s eta 0:00:00
+Downloading types_requests-2.32.0.20241016-py3-none-any.whl (15 kB)
+Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
+Downloading GitPython-3.1.44-py3-none-any.whl (207 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 207.6/207.6 kB 5.2 MB/s eta 0:00:00
+Downloading lightning_utilities-0.12.0-py3-none-any.whl (28 kB)
+Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 79.5/79.5 kB 2.4 MB/s eta 0:00:00
+Downloading sentry_sdk-2.20.0-py2.py3-none-any.whl (322 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 322.6/322.6 kB 6.9 MB/s eta 0:00:00
+Downloading torchmetrics-1.6.1-py3-none-any.whl (927 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 927.3/927.3 kB 14.5 MB/s eta 0:00:00
+Downloading urllib3-2.3.0-py3-none-any.whl (128 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 128.4/128.4 kB 4.1 MB/s eta 0:00:00
+Downloading frozendict-2.4.6-py311-none-any.whl (16 kB)
+Downloading setproctitle-1.3.4-cp311-cp311-macosx_10_9_universal2.whl (16 kB)
+Downloading gitdb-4.0.12-py3-none-any.whl (62 kB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 2.2 MB/s eta 0:00:00
+Downloading smmap-5.0.2-py3-none-any.whl (24 kB)
+Building wheels for collected packages: fairscale, modelcif, antlr4-python3-runtime, ihm
+  Building wheel for fairscale (pyproject.toml) ... done
+  Created wheel for fairscale: filename=fairscale-0.4.13-py3-none-any.whl size=332156 sha256=3ede1c2291f5f6b09d62a36695c4c9250859b36c640d9fcd0e2ddf99fb7a7ce3
+  Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/95/ef/96/5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273
+  Building wheel for modelcif (setup.py) ... done
+  Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41187 sha256=ffeb8ba2c058dca784bb74a9e91f3210826944eeaece3de4c80c69a9f5659770
+  Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/d2/3a/8c/e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df
+  Building wheel for antlr4-python3-runtime (setup.py) ... done
+  Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144554 sha256=5a4205dda4ab01f28989906b79caaca2658ccbd40e312bfcea5dd139ba8f310e
+  Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/1a/97/32/461f837398029ad76911109f07047fde1d7b661a147c7c56d1
+  Building wheel for ihm (setup.py) ... done
+  Created wheel for ihm: filename=ihm-1.8-cp311-cp311-macosx_10_9_x86_64.whl size=194880 sha256=4937e5d722d0d8f12b399d018666e98e070d6821743b4275bb68fed2605a2a06
+  Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/04/b2/4d/f14324777ef987a2137e6bd184eab20679aeadf9d3ad67d198
+Successfully built fairscale modelcif antlr4-python3-runtime ihm
+Installing collected packages: dm-tree, antlr4-python3-runtime, urllib3, smmap, setproctitle, pyyaml, numpy, mashumaro, lightning-utilities, ihm, frozendict, einops, docker-pycreds, click, types-requests, torch, sentry-sdk, scipy, requests, omegaconf, modelcif, gitdb, einx, biopython, torchmetrics, hydra-core, gitpython, fairscale, wandb, pytorch-lightning, boltz
+  Attempting uninstall: urllib3
+    Found existing installation: urllib3 1.26.16
+    Uninstalling urllib3-1.26.16:
+      Successfully uninstalled urllib3-1.26.16
+  Attempting uninstall: pyyaml
+    Found existing installation: PyYAML 6.0
+    Uninstalling PyYAML-6.0:
+      Successfully uninstalled PyYAML-6.0
+  Attempting uninstall: numpy
+    Found existing installation: numpy 1.26.4
+    Uninstalling numpy-1.26.4:
+      Successfully uninstalled numpy-1.26.4
+  Attempting uninstall: click
+    Found existing installation: click 8.0.4
+    Uninstalling click-8.0.4:
+      Successfully uninstalled click-8.0.4
+  Attempting uninstall: scipy
+    Found existing installation: scipy 1.15.1
+    Uninstalling scipy-1.15.1:
+      Successfully uninstalled scipy-1.15.1
+  Attempting uninstall: requests
+    Found existing installation: requests 2.31.0
+    Uninstalling requests-2.31.0:
+      Successfully uninstalled requests-2.31.0
+ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
+tables 3.8.0 requires blosc2~=2.0.0, which is not installed.
+tables 3.8.0 requires cython>=0.29.21, which is not installed.
+conda-repo-cli 1.0.75 requires requests_mock, which is not installed.
+spyder 5.4.3 requires pyqt5<5.16, which is not installed.
+spyder 5.4.3 requires pyqtwebengine<5.16, which is not installed.
+gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed.
+conda-repo-cli 1.0.75 requires clyent==1.2.1, but you have clyent 1.2.2 which is incompatible.
+conda-repo-cli 1.0.75 requires PyYAML==6.0.1, but you have pyyaml 6.0.2 which is incompatible.
+conda-repo-cli 1.0.75 requires requests==2.31.0, but you have requests 2.32.3 which is incompatible.
+numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.3 which is incompatible.
+python-lsp-black 1.2.1 requires black>=22.3.0, but you have black 0.0 which is incompatible.
+anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible.
+aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible.
+Successfully installed antlr4-python3-runtime-4.9.3 biopython-1.84 boltz-0.4.1 click-8.1.7 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 ihm-1.8 lightning-utilities-0.12.0 mashumaro-3.14 modelcif-1.2 numpy-1.26.3 omegaconf-2.3.0 pytorch-lightning-2.4.0 pyyaml-6.0.2 requests-2.32.3 scipy-1.13.1 sentry-sdk-2.20.0 setproctitle-1.3.4 smmap-5.0.2 torch-2.2.2 torchmetrics-1.6.1 types-requests-2.32.0.20241016 urllib3-2.3.0 wandb-0.18.7
+(base) supremestudier@Evans-MBP AMS_548 % pip install --upgrade pip
+Requirement already satisfied: pip in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (23.2.1)
+Collecting pip
+  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/85/8a/1ddf40be20103bcc605db840e9ade09c8e8c9f920a03e9cfe88eae97a058/pip-25.0-py3-none-any.whl.metadata
+  Downloading pip-25.0-py3-none-any.whl.metadata (3.7 kB)
+Downloading pip-25.0-py3-none-any.whl (1.8 MB)
+   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 10.9 MB/s eta 0:00:00
+Installing collected packages: pip
+  Attempting uninstall: pip
+    Found existing installation: pip 23.2.1
+    Uninstalling pip-23.2.1:
+      Successfully uninstalled pip-23.2.1
+Successfully installed pip-25.0
+(base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U
+Requirement already satisfied: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1)
+Requirement already satisfied: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2)
+Requirement already satisfied: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3)
+Requirement already satisfied: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2)
+Requirement already satisfied: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0)
+Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
+Requirement already satisfied: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8)
+Requirement already satisfied: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3)
+Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
+Requirement already satisfied: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016)
+Requirement already satisfied: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0)
+Requirement already satisfied: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0)
+Requirement already satisfied: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13)
+Requirement already satisfied: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14)
+Requirement already satisfied: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2)
+Requirement already satisfied: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7)
+Requirement already satisfied: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7)
+Requirement already satisfied: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2)
+Requirement already satisfied: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84)
+Requirement already satisfied: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1)
+Requirement already satisfied: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (1.11.1)
+Requirement already satisfied: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6)
+Requirement already satisfied: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0)
+Requirement already satisfied: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3)
+Requirement already satisfied: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
+Requirement already satisfied: typing-extensions>=4.1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from mashumaro==3.14->boltz) (4.12.2)
+Requirement already satisfied: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8)
+Requirement already satisfied: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
+Requirement already satisfied: fsspec>=2022.5.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (2024.12.0)
+Requirement already satisfied: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1)
+Requirement already satisfied: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0)
+Requirement already satisfied: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
+Requirement already satisfied: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
+Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0)
+Requirement already satisfied: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
+Requirement already satisfied: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0)
+Requirement already satisfied: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44)
+Requirement already satisfied: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
+Requirement already satisfied: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
+Requirement already satisfied: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
+Requirement already satisfied: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0)
+Requirement already satisfied: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4)
+Requirement already satisfied: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
+Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
+Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
+Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
+Requirement already satisfied: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
+Requirement already satisfied: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
+Requirement already satisfied: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
+Requirement already satisfied: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
+Requirement already satisfied: six>=1.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz) (1.16.0)
+Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (3.8.5)
+Requirement already satisfied: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12)
+Requirement already satisfied: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
+Requirement already satisfied: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
+Requirement already satisfied: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->einx==0.3.0->boltz) (1.3.0)
+Requirement already satisfied: attrs>=17.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (22.1.0)
+Requirement already satisfied: multidict<7.0,>=4.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (6.0.2)
+Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (4.0.2)
+Requirement already satisfied: yarl<2.0,>=1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.8.1)
+Requirement already satisfied: frozenlist>=1.1.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.3.3)
+Requirement already satisfied: aiosignal>=1.1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.2.0)
+Requirement already satisfied: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2)
+(base) supremestudier@Evans-MBP AMS_548 % pip check
+tables 3.8.0 requires blosc2, which is not installed.
+tables 3.8.0 requires cython, which is not installed.
+conda-repo-cli 1.0.75 requires requests-mock, which is not installed.
+spyder 5.4.3 requires pyqt5, which is not installed.
+spyder 5.4.3 requires pyqtwebengine, which is not installed.
+gensim 4.3.0 requires fuzzytm, which is not installed.
+conda-repo-cli 1.0.75 has requirement clyent==1.2.1, but you have clyent 1.2.2.
+conda-repo-cli 1.0.75 has requirement PyYAML==6.0.1, but you have pyyaml 6.0.2.
+conda-repo-cli 1.0.75 has requirement requests==2.31.0, but you have requests 2.32.3.
+numba 0.57.0 has requirement numpy<1.25,>=1.21, but you have numpy 1.26.3.
+python-lsp-black 1.2.1 has requirement black>=22.3.0, but you have black 0.0.
+anaconda-cloud-auth 0.1.3 has requirement pydantic<2.0, but you have pydantic 2.10.6.
+s3fs 2023.4.0 has requirement fsspec==2023.4.0, but you have fsspec 2024.12.0.
+aiobotocore 2.5.0 has requirement botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99.
+conda-verify 3.4.2 is not supported on this platform
+(base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U --use-deprecated=legacy-resolver
+Requirement already up-to-date: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1)
+Requirement already satisfied, skipping upgrade: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2)
+Requirement already satisfied, skipping upgrade: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3)
+Requirement already satisfied, skipping upgrade: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2)
+Requirement already satisfied, skipping upgrade: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0)
+Requirement already satisfied, skipping upgrade: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
+Requirement already satisfied, skipping upgrade: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8)
+Requirement already satisfied, skipping upgrade: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3)
+Requirement already satisfied, skipping upgrade: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
+Requirement already satisfied, skipping upgrade: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016)
+Requirement already satisfied, skipping upgrade: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0)
+Requirement already satisfied, skipping upgrade: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0)
+Requirement already satisfied, skipping upgrade: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13)
+Requirement already satisfied, skipping upgrade: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14)
+Requirement already satisfied, skipping upgrade: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2)
+Requirement already satisfied, skipping upgrade: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7)
+Requirement already satisfied, skipping upgrade: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7)
+Requirement already satisfied, skipping upgrade: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2)
+Requirement already satisfied, skipping upgrade: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84)
+Requirement already satisfied, skipping upgrade: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1)
+Requirement already satisfied, skipping upgrade: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
+Requirement already satisfied, skipping upgrade: typing-extensions>=4.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (4.12.2)
+Requirement already satisfied, skipping upgrade: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (1.11.1)
+Requirement already satisfied, skipping upgrade: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
+Requirement already satisfied, skipping upgrade: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
+Requirement already satisfied, skipping upgrade: fsspec in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (2024.12.0)
+Requirement already satisfied, skipping upgrade: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0)
+Requirement already satisfied, skipping upgrade: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3)
+Requirement already satisfied, skipping upgrade: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
+Requirement already satisfied, skipping upgrade: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
+Requirement already satisfied, skipping upgrade: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1)
+Requirement already satisfied, skipping upgrade: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0)
+Requirement already satisfied, skipping upgrade: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
+Requirement already satisfied, skipping upgrade: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
+Requirement already satisfied, skipping upgrade: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
+Requirement already satisfied, skipping upgrade: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0)
+Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
+Requirement already satisfied, skipping upgrade: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
+Requirement already satisfied, skipping upgrade: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
+Requirement already satisfied, skipping upgrade: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
+Requirement already satisfied, skipping upgrade: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6)
+Requirement already satisfied, skipping upgrade: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8)
+Requirement already satisfied, skipping upgrade: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0)
+Requirement already satisfied, skipping upgrade: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44)
+Requirement already satisfied, skipping upgrade: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
+Requirement already satisfied, skipping upgrade: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0; sys_platform != "linux" in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
+Requirement already satisfied, skipping upgrade: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
+Requirement already satisfied, skipping upgrade: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0)
+Requirement already satisfied, skipping upgrade: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4)
+Requirement already satisfied, skipping upgrade: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
+Requirement already satisfied, skipping upgrade: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->torch>=2.2->boltz) (1.3.0)
+Requirement already satisfied, skipping upgrade: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
+Requirement already satisfied, skipping upgrade: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas>=2.2.2->boltz) (1.16.0)
+Requirement already satisfied, skipping upgrade: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
+Requirement already satisfied, skipping upgrade: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12)
+Requirement already satisfied, skipping upgrade: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2)
+(base) supremestudier@Evans-MBP AMS_548 % conda activate
+(base) supremestudier@Evans-MBP AMS_548 % conda env list
+# conda environments:
+#
+base                  *  /Users/supremestudier/anaconda3
+sage-dev                 /Users/supremestudier/anaconda3/envs/sage-dev
+                         /Users/supremestudier/opt/anaconda3
+(base) supremestudier@Evans-MBP AMS_548 % which boltz
+/Users/supremestudier/anaconda3/bin/boltz
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ home
+(base) [ehspector@milan1 espector]$ cd 4s0v/
+(base) [ehspector@milan1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@milan1 gas_teiger]$ cd no_charge/
+(base) [ehspector@milan1 no_charge]$ ls
+s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
+s0v.lig_no_charge.min_scored.mol2     gas_2.out
+s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
+(base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2
+(base) [ehspector@milan1 no_charge]$ ls
+s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
+s0v.lig_no_charge.min_scored.mol2     gas_2.out
+s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
+(base) [ehspector@milan1 no_charge]$ cd ..
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@milan1 gas_teiger]$ vi gas.in
+(base) [ehspector@milan1 gas_teiger]$ cd ..
+(base) [ehspector@milan1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@milan1 4s0v]$ cd energy_min/
+(base) [ehspector@milan1 energy_min]$ ls
+s0v.lig.min_scored.mol2  min.in  min.out
+(base) [ehspector@milan1 energy_min]$ vi 4s0v.lig.min_scored.mol2
+(base) [ehspector@milan1 energy_min]$ cd ..
+(base) [ehspector@milan1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out
+(base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@milan1 gas_teiger]$ cd no_charge/
+(base) [ehspector@milan1 no_charge]$ ls
+s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
+s0v.lig_no_charge.min_scored.mol2     gas_2.out
+s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
+(base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2
+(base) [ehspector@milan1 no_charge]$ cd ..
+(base) [ehspector@milan1 gas_teiger]$ cd ..
+(base) [ehspector@milan1 4s0v]$ vi  energy_min/4s0v.lig.min_scored.mol2
+(base) [ehspector@milan1 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/test.mol2
+(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas.out  no_charge            no_gas.out  test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi test.mol2
+(base) [ehspector@milan1 gas_teiger]$ cp gas.in gas_2.in
+(base) [ehspector@milan1 gas_teiger]$ pwd
+/gpfs/projects/rizzo/espector/4s0v/gas_teiger
+(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
+(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
+(base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas_2.in   gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
+gas_2.out  gas.out  no_charge            no_gas.out  test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas_2.out
+(base) [ehspector@milan1 gas_teiger]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ home
+(base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@milan2 gas_teiger]$ ls
+gas_2.in   gas.out              no_gas.in               test.mol2
+gas_2.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+gas.in     no_charge            no_gas.out_scored.mol2
+(base) [ehspector@milan2 gas_teiger]$ vi gas_2.in
+(base) [ehspector@milan2 gas_teiger]$ cp gas_2.in gas_3.in
+(base) [ehspector@milan2 gas_teiger]$ vi gas_3.in
+(base) [ehspector@milan2 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out
+(base) [ehspector@milan2 gas_teiger]$ ls
+gas_2.in   gas_3.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+gas_2.out  gas.in     no_charge            no_gas.out_scored.mol2
+gas_3.in   gas.out    no_gas.in            test.mol2
+(base) [ehspector@milan2 gas_teiger]$ vi gas_3.out
+(base) [ehspector@milan2 gas_teiger]$ vi gas_3.in
+(base) [ehspector@milan2 gas_teiger]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ ls
+  5EEN  class_project  class_work
+(base) [ehspector@milan2 AMS_536]$ cd class_
+-bash: cd: class_: No such file or directory
+(base) [ehspector@milan2 AMS_536]$ cd class_work/
+(base) [ehspector@milan2 class_work]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 class_work]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ mkdir Tutorials
+(base) [ehspector@milan2 AMS_536]$ mv class_work/ Tutorials/
+(base) [ehspector@milan2 AMS_536]$ ls
+  5EEN  class_project  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+class_work
+(base) [ehspector@milan2 Tutorials]$ mv class_work/ 2w26
+(base) [ehspector@milan2 Tutorials]$ ls
+w26
+(base) [ehspector@milan2 Tutorials]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ mv 1086/ 5EEN/ Tutorials/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 2w26]$ cd 001
+-bash: cd: 001: No such file or directory
+(base) [ehspector@milan2 2w26]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
+w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
+(base) [ehspector@milan2 001_structure]$ rm *.mol2
+(base) [ehspector@milan2 001_structure]$ ls
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm selected_spheres.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_new_surface.dms
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+INSPH  OUTSPH  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+INSPH  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ rm 2w26.box.pdb
+(base) [ehspector@milan2 003_gridbox]$ rm grid.out
+(base) [ehspector@milan2 003_gridbox]$ mv 01showbox.sh showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+ grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 2w26]$ cd 004_dock/
+(base) [ehspector@milan2 004_dock]$ ls
+(base) [ehspector@milan2 004_dock]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 5EEN/commands.txt
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/
+(base) [ehspector@milan2 5EEN]$ ls
+commands.txt
+(base) [ehspector@milan2 5EEN]$ bash commands.txt
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 5EEN]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/001_structure/
+(base) [ehspector@milan1 001_structure]$ pwd
+/gpfs/home/ehspector/AMS_536/Tutorials/5EEN/001_structure
+(base) [ehspector@milan1 001_structure]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd 001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een_surface.dms
+(base) [ehspector@milan1 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+INSPH  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/002_surface_spheres/sphere.sph 5EEN/002_surface_spheres/sphere.sph
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een_surface.dms  INSPH  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph
+Press ENTER or type command to continue
+(base) [ehspector@milan1 002_surface_spheres]$ bash sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een.sph  5een_surface.dms  INSPH  OUTSPH  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 5EEN]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een.sph  5een_surface.dms  INSPH  OUTSPH  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+INSPH  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een.sph  5een_surface.dms  INSPH  OUTSPH  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd 001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ bash selected_sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een.sph          INSPH   selected_sphere.sph   sphere.sph
+een_surface.dms  OUTSPH  selected_spheres.sph
+(base) [ehspector@milan1 002_surface_spheres]$ mv selected_sphere.sph select.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi selected_spheres.sph
+(base) [ehspector@milan1 002_surface_spheres]$ cd ..
+(base) [ehspector@milan1 5EEN]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan1 5EEN]$ mv 004_dock/ 004_energymin
+(base) [ehspector@milan1 5EEN]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ ls
+ grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/showbox.sh 5EEN/003_gridbox/showbox.sh
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/
+(base) [ehspector@milan1 5EEN]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ ls
+showbox.in  showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ vi showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ bash showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ vi grid.in
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   grid.in   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ rm grid.in
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ ls
+ grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ vi grid.in
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.in 5EEN/003_gridbox/grid.in
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.sh 5EEN/003_gridbox/grid.sh
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd 001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ vi grid.
+(base) [ehspector@milan1 003_gridbox]$ vi grid.in
+(base) [ehspector@milan1 003_gridbox]$ vi grid.in
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ vi grid.in
+(base) [ehspector@milan1 003_gridbox]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan1 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan1 003_gridbox]$ bash grid.sh
+(base) [ehspector@milan1 003_gridbox]$ ls
+een.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
+ grid.bmp       grid.nrg   grid.sh   '&showbox.log&'
+(base) [ehspector@milan1 003_gridbox]$ vi grid.out
+(base) [ehspector@milan1 003_gridbox]$ cd ../004_energymin/
+(base) [ehspector@milan1 004_energymin]$ ls
+(base) [ehspector@milan1 004_energymin]$ touch min.in
+(base) [ehspector@milan1 004_energymin]$ ls
+min.in
+(base) [ehspector@milan1 004_energymin]$ dock6 -i min.in
+--------------------------------------
+DOCK v6.12
+Released April 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):yes
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+                                             ligand_atom_file [database.mol2] ():../001_structure/5een_ligand_H_cH.mol2
+                                            limit_max_ligands [no] (yes no):
+                                                skip_molecule [no] (yes no):
+                                           read_mol_solvation [no] (yes no):
+                                               calculate_rmsd [no] (yes no):yes
+                                       use_rmsd_reference_mol [no] (yes no):yes
+                                      rmsd_reference_filename [ligand_rmsd.mol2] ():../001_structure/5een_ligand_H_cH.mol2
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):
+                                     grid_score_rep_rad_scale [1] ():
+                                         grid_score_vdw_scale [1] ():
+                                          grid_score_es_scale [1] ():
+                                          grid_lig_efficiency [no] (yes no):
+                                       grid_score_grid_prefix [grid] ():../003_gridbox/grid
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+                                              minimize_ligand [yes] (yes no):
+                                       simplex_max_iterations [1000] ():
+                               simplex_tors_premin_iterations [0] ():
+                                           simplex_max_cycles [1] ():
+                                       simplex_score_converge [0.1] ():
+                                       simplex_cycle_converge [1.0] ():
+                                           simplex_trans_step [1.0] ():
+                                             simplex_rot_step [0.1] ():
+                                            simplex_tors_step [10.0] ():
+                                            simplex_final_min [no] (yes no):
+                                          simplex_random_seed [0] ():
+                                        simplex_restraint_min [no] (yes no):yes
+                                simplex_coefficient_restraint [10.0] ():
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+                                                   atom_model [all] (all | united):
+                                                vdw_defn_file [vdw.defn] ():defn
+                                               flex_defn_file [flex.defn] ():defn
+                                              flex_drive_file [flex_drive.tbl] ():defn
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+                                        ligand_outfile_prefix [output] ():5een.lig.min
+                                          write_mol_solvation [no] (yes no):
+                                           write_orientations [no] (yes no):
+                                        num_scored_conformers [1] ():
+                                              score_threshold [100.0] ():
+                                                 rank_ligands [no] (yes no):
+------------------------------------------------------------------------------------------
+Could not open defn for reading.  Program will terminate.
+(base) [ehspector@milan1 004_energymin]$ ls
+min.in
+(base) [ehspector@milan1 004_energymin]$ vi min.in
+(base) [ehspector@milan1 004_energymin]$ cd ../../
+(base) [ehspector@milan1 Tutorials]$ cd ../../
+(base) [ehspector@milan1 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan1 ~]$ cd
+(base) [ehspector@milan1 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan1 ~]$ cd ..
+(base) [ehspector@milan1 home]$ ls
+cd ..aaachase              dbluestein          jkottmann      msavenkov         skomatireddy
+aaaggarwal            dbobo               jksullivan     msayana           skoppuravuri
+aaaggarwal.26FEB2020  dcalabria           jktsui         msazonova         skorada
+aabdurrob             dcazorla            jleehand       mschedel          skotelnikov
+aabhilash             dcbrown             jlfong         mschrimpf         skotla
+aadarsh               dcharan             jlguerra       mschwaller        skrichevsky
+aadubois              dchien              jlipshultz     mshaaban          skristam
+aagashe               ddassanis           jlomanto       mshahneousba      skrupp
+aagishtein            ddelayo             jluceno        mshih             sladerwager
+aahern                ddemartini          jlungu         mshinder          slakshminara
+aaiyer                ddukes              jlutsky        mshu              slaverty
+aajith                deachen             jlweissman     msilfies          slthomas
+aakale                decarlson           jmaghakian     msmoawad          smadishetty
+aakiti                dekblom             jmarcantonio   msrao             smaiti
+aakkumar              delam               jmarciano      msreeves          smallipattu
+aaksenova             demccabe            jmayortorres   mstanacevic       smamalis
+aaliang               dereliu             jmeliker       msweber           smartynenko
+aallin                deroy               jmendezmende   mtalukder         smascarenhas
+aallu                 devlin              jmgentile      mthu              smconnors
+aalpern               dfarahmandpo        jmiao          mtoledorozyc      smdick
+aamahmood             dfei                jmitchell      mtsonev           smedved
+aambrown              dfucich             jmorkos        mturk             smeghdadizan
+aamgalan              dgaidhani           jmulackal      mumarani          smelhiraj
+aaminev               dgenet              jmurrugarral   muprit            smesiha
+aamurthy              dgersappe           jmurzaku       mvalakonda        smhenry
+aanaggarwal           dg-mgmt1-auth-keys  jmvasquez      mvashishtha       smiduthuri
+aanagnostopo          dg-mgmt2-auth-keys  jnassar        mvfernandezs      smilakovic
+aanik                 dgnatenko           jnatarajan     mvilensky         smirghafouri
+aaprasad              dgoon               jnery          mwilking          smirroshande
+aarasappan            dgruzdev            jnicasio       myarif            smofakham
+aarefin               dgursoy             jnmauro        myearsley         smui
+aarmas                dgwood              jnong          myoungblood       smukherjee
+aarroyave             dhailegeorgi        joawilson      mysql             smvaccaro
+aasim                 dhamam              jocai          mzamani           snarmeen
+aaslov                dhandzlik           jocwilliams    mzepedaaguil      snigam
+aates                 dhdesouza           jodey          mzhang            snikhil
+aaurora               dhildreth           jodoh          naahassan         snimatullo
+aavadhani             dhongyi             jodweinstein   nabchowdhury      snizambad
+aavira                dhperumal           joeleung       nabsyed           snolas
+aaydin                dhualong            joeychan       nacchen           snyman
+aaysheth              diannace            jofranklin     nacharya          soba
+ababbar               disandovalch        johbernard     nagnihotri        sochakrabort
+abadhe                diwliu              johnliu        nagutierrez       sohshin
+abahadori             djagnarain          joifan         nalewis           sohtsuka
+abaidya               djgold              jomyoung       nanqwang          solhapark
+aball                 djlambert           jonamartins    napopova          somishra
+abardizbania          djoh                jonicholson    naqiu             somunoz
+abbhaskar             djulian             jonsu          nasweet           sooapark
+abeahmad              djyu                jonyin         natsai            sopjang
+abenslama             dkadams             joolee         nazzhou           sortizbetanc
+abialkowska           dkharzeev           joosuh         nbalasubrama      sosarangi
+abjoshi               dkirby              joroiland      nbasok            sosuresh
+abkanevsky            dkozakov            joshmathew     nbayas            sowu
+abogetti              dkunjadiya          joshumartin    nbodduluri        sozturk
+aborad                dlanger             jovvazquezri   nbosviel          spaci
+aborcatasciu          dlhe                joying         nbowers           spandrekar
+aborger               dlucksted           jozhao         nciotoli          spang
+aborowicz             dmahalli            jpantano       ncmeloottu        spapazahario
+abozin                dmahzabin           jparise        ncpathak          spapazis
+abphilip              dmale               jparkinson     ndcertain         sparvathredd
+abrady                dmarkov             jpascal        ndev              spathrose
+absalem               dmarr               jpcastillo     ndheilly          spilkey
+abtambe               dmckinnon           jperezrios     ndigrandi         spiret
+aburford              dmirfenderes        jpeshansky     ndnguyen          splee
+acage                 dmorenosanti        jpitt          ndokania          spochron
+acalder               dmukherjee          jpmoryl        ndurand           spothumahant
+acali                 dmulbagalven        jporavanthat   ndzikowski        spriyadarsha
+acamino               dnanjappa           jpwhite        nesteves          spugach
+acastiblanco          dnimatullo          jqxiao         nexposescan       sqavi
+accapua               dnterry             jranjan        neyang            srahmani
+acchakravart          dobyrne             jrawski        nezheng           sraisinghani
+acherath              dochoi              jrcheung       nfaiza            sramanarajan
+achouhan              dofu                jrcorbett      nfpugliese        sramanarajan.OLD
+acmarra               dohhlee             jrest          nganu             sramjan
+adamare               dokkang             jrgorman       nghoang           sramstrom
+adanial               dongsong            jrimel         ngitman           srashidian
+adanoji               dongwhan            jrkamler       ngluck            sretineni
+adharan               donshi              jrleeman       ngujarati         srgupte
+adiloreto             dotan               jrojahn        nhamdan           srnalluri
+ading                 doyjang             jrutledge      nhirtle           srpayne
+admannino             dozhong             jrwei          nichaturvedi      srshende
+adpeng                dpadhorny           jsaldivar      nidimeglio        ssabaghian
+adpollack             dpare               jsalley        nigreen           ssagynbayeva
+adrana                dparedesmeri        jsaltz         nileong           ssandal
+adrflorio             dparwana            jsaputo        niranmanesh       ssarnot
+adrogers              dpati               jsaxena        nisankar          ssarwar
+adubey                dpatil              jscanderson    nisong            sseepersaud
+adutt                 dpenchoff           jschuchart     nisoni            ssemerkant
+aecuomo               dpfennell           jschwedes      nivsingh          sserbin
+aeichert              dpotemkin           jseeliger      njschwartzap      sshaharia
+aeltareb              drendina            jseol          nkahmed           sshapourmian
+aeweiss               drhamilton          jsgordon       nkandru           ssheikhi
+afahmed               dschneble           jsinanan       nkatla            sshoque
+afarhadzadeh          dseddoh             jsistla        nkdean            sshrestha
+afgregory             dsforza             jskowalski     nkeer             sshrivastava
+afrigo                dshangase           jslogan        nkhalsa           ssivalenka
+afurey                dsingla             jsmaers        nkhandagale       ssjohn
+agaffoor              dsli                jsmucker       nkhatri           sskiena
+agaikwad              dslo                jsteier        nkinalis          ssomani
+agarforth             dsmolarski          jsuchan        nkinlock          ssperrottet
+agargueta             dstepanenko         jtalaveragre   nkyose            sstoller
+agauer                dstrenski           jtekverk       nleak             sstoyanov
+aghai                 dswesty             jtepan         nlogozzo          ssundar
+agilgomez             dthanassi           jtevans        nlrogers          ssunia
+agmaharaj             dtpham              jtgabrielli    nmahamud          ssyedfahad
+agnsinha              dtsybychev          jtjones        nmaher            ssyritsyn
+agopalkrishn          dtung               jtmessina      nmanzella         staralekar
+agraikos              duwwang             jtrelewicz     nmarcella         stawong
+agugel                dvahabli            jtrue          nmathew           stelehany
+agulhane              dvyas               juaalcantara   nmehanna          sthaker
+ahalwah               dwhitty             juffeng        nmeister          sthorgusen
+ahc                   dwiczer             julima         nmenasche         stjjiang
+ahmkhan               dwillcox            juliwu         nmendiratta       stmandell
+ahomayounnik          dzavala             jumma          nmeruva           stmccabe
+ahsingh               dziadlou            junding        nmichielsen       stomar
+ahurtado              eadas               jungshwang     nmitra            stpak
+ahxiao                earavera            junholee       nnadkarni         strainer
+aicheng               eatkinson           junhuzhang     nnaitlho          ststern
+aidnani               ebagherizade        junhyelee      nnakka            stuznik
+ailyu                 ebartlett           junjiang       nnawal            stzeng
+airussell             eboria              junkang        nnehaindrani      stzou
+ajacovelli            ebreen              junszhou       nnghiemvu         sudkhan
+ajalwan               ebremer             juntyao        nniemiec          sukkumar
+ajamieson             ebrini              junwang5       noibrahim         sunarasimhas
+ajasniew              ebryski             junxialiu      nolconner         sunarasimhas.OLD
+ajchan                ecarcelespov        junywang       novsingh          sunghucho
+ajchavez              ecgross             jusandoval     npahlavan         sunkim2
+ajhong                echurch             juschan        npanagodawet      surmy
+ajkoller              eclemmon            jusliu         nparghi           sushahid
+ajlli                 ecline              jusong         npasari           suwei
+ajmasella             ecoutsias           justili        npayen            svadnerkar
+ajoung                ecowley             jusu           npomata           svaldez
+ajscarlatos           edeturk             juychen        npregosin         svanderpoel
+ajtran                edma                juyyan         nrajput           svayasi
+ajwelsh               edowney             juzou          nramdin           svee
+ajyadav               edzhang             jvansnellenb   nreaton           swaxman
+akalugade             eeryildiz           jvaska         nsalekfarama      swchaudhury
+akanodia              efinson             jverbaarscho   nsampson          swen
+akapote               egebb               jvishal        nsehgal           sweverma
+akarkare              egentles            jvpepe         nshouman          swpaul
+akarzai               egouvis             jvu            nsimakov          sxchen
+akaufman              eheywood            jwahhab        nsipperly         syaddanapudi
+akhibovska            ehspector           jwcross        nsmehta           syalla
+akhosronejad          ejcarey             jwcusick       nsoder            syarma
+akhoukhi              ejguan              jwisdom        nsokolow          syatigala
+akingan               ejli                jwlodek        nsomani           syatskar
+akirillov             ejohnfelt           jxue           nstreb            sydiaz
+akkale                ekandov             jyerrick       ntadler           syousef
+akonosky              ekbetancourt        jyluo          ntardugno         sytlee
+akravchuk             ekeck               jzoodsma       ntetrault         tabhatia
+akrowe                ekeough             kabichandani   ntippabhatla      tadoyle
+aktyagi               ekhew               kadeng         ntripti           taeklee
+akucich               eklau               kadiallo       nvafaeinajaf      taeyounkim
+akuduregundi          ekoo                kadill         nvitek            tagiles
+akundhuru             elari               kadreher       nvohra            tahkhan
+akverma               elettieri           kafarber       nvsutherland      tajjung
+akwakye               elgchan             kaifzheng      nwein             takther
+alabella              elharris            kaili          nwweber           talama
+alaing                eli                 kailiu2        nxlee             talare
+alanhuang             ellai               kailjiang      nyfletcher        talin
+alchung               elleisenberg        kaimxu         obellinson        tallison
+aldong                elmlowe             kaitong        odeshpande        tamislam
+aldraper              elogeswar           kaixichen      odiamond          tanis
+alehsu                elslattery          kamhassan      odickerson        taryu
+alem                  emacosta            kamrivera      oeskiocak         tbabu
+alexhernande          emarants            kanagarwal     ohaputhanthr      tbertino
+alfwu                 emarkowitz          kanzhao        ohyejin           tbrackins
+algrullon             emarzigliano        kapatel        okim              tbrinckmann
+alhhuang              embriggs            kaporter       okoren            tbrinkley
+alianwar              emrlin              kapu           omcgranaghan      tburfeind
+alicwang              emroberts           karamachandr   omorozova         tbushra
+alietzau              emyhand             kargill        omoy              tcanli
+alifeng               enebet              kasong         onatu             tchatterton
+aliguori              eoruro              katalwar       oogunfolakan      tchristy
+alindquist            eozkirimli          katschmidt     ooreilly          tchugh
+allekim               epapadopoulo        kbaylous       orambow           tcotroneo
+allelin               erandhawa           kbdiaz         osdeshpande       tdawar
+allwong               eraut               kbeckerredd    oshakkour         tdiprima
+almabraham            erbraun             kbelfon        oshetty           tdviri
+almishra              erfan               kberard        osteele           tema
+alokre                erglukhov           kberghaus      oyang             testro
+alowell               ericlin1            kccoughlin     oyasar            tgavryshko
+alperezmendo          erizhou             kchetan        padari            tglotch
+alqin                 erkumar             kchitale       paggarwal         tgrgas
+alsli                 erluo               kdas           pahan             tgrossberndt
+alvhsu                erosenberg          kdavidson      pallen            tguttula
+alynegron             errjones            kdehmelt       pamishra          thamada
+amacinnis             erschroeder         kdemir         parjain           thausch
+amaffei               erwhuang            kdevedzhiev    parmitage         thdavidson
+amanagarwal           esahin              kdhar          patflanagan       therault
+amanpsingh            esalman             kdhuri         patmuller         therodrigues
+amanzoor              esaraivanov         kdyro          pavkirkar         thollis
+amaresca              eschiltzrous        kebui          pavnkaur          thomlin
+amarya                eshaji              keckartt       pawu              thren
+amassari              eshetreatkle        kelam          payao             thzhou
+amasuno               eshih               keliao         pb                tianyuawang
+ambbrown              eshuryak            kellywang      pbaliga           tili
+amccumber             esicoli             kelvlin        pcascantebon      timji
+amcelroy              esiegmann           kenchin        pcastillo         timshi
+amchale               esogut              kenhu          pchinthamred      tinggao
+amcpherran            esonmez             kennwu         pdalaya           tinghwu
+amehla                essingh             kereid         pdamore           tingliu2
+amehmood              eswong              kerwood        pdevarajan        tingslin
+amgondal              etakeuchi           kevazquez      pdjuric           tinliu
+amibrahim             etalis              kevcai         pdonat            tiwwong
+amigues               etchan              kevcheng       pdongle           tixi
+amisaha               etcheung            keviliu        pdutta            tiyuan
+amkgupta              ethresher           kevwei         pechang           tjarrett
+amnoonan              etmonaco            kexi           peihsieh          tjohannessen
+amohamed              etrommer            kfatema        peinwang          tkarwal
+amohammadrez          etsang              kfernando      penzhang          tknoll
+amohanty              etwest              kflora         pesun             tkohlmann
+amohideen             etyen               kfryer         pferrero          tkral
+amoonilal             evalin              kgarg          pgaikar           tkurc
+amrabet               evaxie              kgayadhankar   pganapathi        tla
+amramroop             evergaracobo        kgcassar       pganesh           tlata
+amrangwala            evxie               kgjonas        pgodoy            tloden
+amritpsingh           ewpeterson          kgoranta       pgoldbart         tlonsway
+amullhaupt            exiu                kgulati        pgoriparthi       tmcgee
+amychen5              eylei               khajny         pgubbala          tmia
+amyla                 eyzhu               khasegawa      pguo              tmohandas
+anadelgado            fabdinov            khoh           pgurung           tmoriya
+analekseenko          faliang             khumphries     phariprasad       tmsmyth
+anarora               falmodaresit        khyunjae       phowlader         tmuntean
+ancollins             faluo               kihan          phtnguyen         tnle
+andcheung             fang1               kim128         phyeh             tnsingletary
+andguo                fanliu2             kim169         pinlee            toneal
+andgutierrez          fannli              kim65          pinliu            toye
+andrchu               fanwang1            kingle         pkaelbling        tpalit
+andrwu                faoki               kipoon         pkayedpour        tqduong
+andylin2              faslanbeigi         kisrani        pkidambi          tqle
+anearora              fatrahman           kissung        pkottapalli       traj
+anegi                 fatsai              kjamal         pkrstic           trichen
+aneiman               faye                kjayanettiar   pkuan             trli
+anejoshi              fayyang             kjroberts      pkwoczak          trosenlicht
+anejoshi.OLD          fbasharat           kjtorres       pliu              tsclement
+anemajerova           fbischoff           kjun           plorenagodoy      tshrestha
+anfrenkel             fcherat             kkamate        pmao              tsinghal
+angderosa             fcornejofern        kkannapur      pmarla            tslewis
+aniksingh             fcoskun             kkasarapu      pmatera           tsmiley
+anisrinivasa          feliang             kkasavajhala   pmcdowall         tteng
+anjmoore              fenzhang            kkaushik       pmdunge           tthakir
+ankmaheshwar          fewang              kkayang        pmeade            tthulasidas
+ankrishnan            feyeh               kkirane        pmeda             ttnnguyen
+anltran               fgao                kkostyszyn     pmmehta           ttom
+annicoll              fhchaudhry          kkui           pmscully          tweinacht
+anpnguyen             fiburke             kkurti         pmuzac            tweiwei
+anpurwar              fiowong             kkyeong        pnalluri          twymore
+ansabharwal           fjalia              klanzetta      pnookala          txiang
+ansgandhi             fjangchup           klhudson       podonnell         tye
+anshen                fkarankumar         kljjohnson     ppolak            tyeh
+anslade               fkhondker           kllivichuzca   ppriyadarshi      tyokoyama
+anthochen             fladeind            kmadanahitib   praagarwal        tzwei
+antmunoz              fluo                kmardysilofa   pragupta          uarora
+antzhu                fmaisha             kmasarik       praroy            uarora.OLD
+anurizada             fmlopez             kmbala         pratagarwal       ugarg
+anvinod               fmnoor              kmchang        pratkumar         ukadakia
+anzaman               fnieto              kmchau         priyjain          umoll
+anzhu                 forabona            kmcneil        prkkumar          umukherjee
+anzzhou               fpocaamoros         kmfallon       prmukhopadhy      upoddar
+aokisamen             frdominguezg        kmhayes        prouth            urasheed
+apaddayurush          frhu                kmsimon        prreddy           urehman
+apaddayurush.OLD      frobayobohor        kmueller       psahu             urosani
+apagarwal             fsotiropoulo        kmungsoo       psamang           ushafiq
+apalit                fuliang             kmurgas        psangtani         ushassan
+apalo                 fwelcome            kpallmann      psekar            usunar
+apalve                fzali               kpinzon        pshanbhogue       utegshbayar
+apamfilie             gacolella           kpipitone      pskota            utumuluri
+aperezantona          gahuja              kprose         psmeyer           uuckun
+apettenati            gakapoor            kralbano       psokol            uyevarouskay
+aphope                gakhan              kramcharan     psonawane         vachandramou
+apilco                galing              krayfield      psoundarapan      vadabala
+apizzulli             garrchen            krdonaldson    pssingh           vanlin
+aplu                  gashna              krisharma      psurana           vanugu
+apolanco              gatran              krjain         psutter           vassingh
+apopoviciu            gaumoithe           krkehrli       ptitle            vbabu
+aporripiredd          gazzhang            krmartin       ptonra            vbayevskiy
+aprabhakar            gbalabhadra         krokosz        ptubiolo          vbrill
+apradeep              gbalazsi            krtan          puzheng           vcacciola
+aprencis              gbangera            ksabo          pvaishnavi        vcarter
+apsinghal             gbermejo            ksampathkuma   pvaska            vchanana
+apytel                gbhattachary        kscardigno     pvemula           vduncan
+araghani              gbiselli            kschweitzer    pvespe            verana
+arahimyar             gbock               kshima         pximello          vgoel
+arahmati              gbosilca            kshou          pyao              vhattibettam
+aranasinghe           gbrill              ksirapu        pzbarrett         vhegde
+aravula               gchurchill          ksoumahoro     qiangwang         vhnguyen
+arbalasubram          gcma                kspuhler       qianywu           vhuynh
+arcurtis              gdhama              ksucich        qiaocwu           vicdai
+ardasgupta            gdjones             kswayze        qicao             vidong
+ardowling             gduarteramos        ktallman       qiding            viguo
+areisel               geliang             kthilanka      qihlin            vikamat
+aresnick              gfiakos             ktsteven       qinie             villi
+arfali                ggandem             ktuzinowski    qinjiang          vima
+argiannakopo          ggeorgi             kuagarwal      qinren            vincewu
+arglenn               ggopalkrishn        kuchan         qinzhao           vinmirandabr
+arhossain             gguleria            kumar1         qipan1            vinzheng
+arjain                ghe                 kumar1.OLD     qirli             visheskumar
+arjkrishna            ghothi              kunli          qirwu             vissharma
+armishra              gibrown             kuraj          qxiong            vivlam
+arobert               gigill              kuzhong        raagarwal         viyee
+arodriguezd           gimbriano           kveeramah      rabasu            vjana
+arojain               gipark              kvshah         rachatterjee      vjishah
+arpahlavan            girizzo             kwahlin        rachatterjee.OLD  vkale
+arpbanerjee           gito                kwwalton       rachowdhury       vkhanikaeva
+arpereira             gjfuentes           kwyu           raclam            vkodumurumee
+arsaxena              gjiang              kwyyoo         radsrinivasa      vkondipati
+arskhan               gjkim               kyadav         raggarg           vkootagaram
+arumar                gkementzidis        kychao         ragte             vlloyd
+aryshrivasta          gkowzan             kyethiraj      rahhuang          vloganathan
+asadana               glarangeira         kylanglois     rahraja           vlokwani
+asaji                 gmichaels           kymjames       raich             vmaurya
+asakhan               gmihalache          kyumin         raiislam          vmontanez
+asamala               gmiles              kzzhang        rairahman         vpakala
+asamanta              gmogol              lahess         rajatkumar        vpamula
+asamavedam            gmoutsanidis        lawlin         rajdas            vperkowski
+asatam                gmuradas            lbai           ramhuang          vranjan
+aschneble             gnarh               lbozarth       ramorosso         vratnala
+aschorer              gnwood              lcaradonna     rannadi           vrustagi
+ashaalan              goconrosario        lchi           rapeaning         vseecharan
+asharfuddin           gparkar             lchrastecka    rashanbhag        vsnu
+asheneman             gperezgonzal        lcolleyndeso   rashizawa         vstaub
+asillato              gprachi             lcooke         ratwi             vtangirala
+asingal               grahme              ldavalosalva   raychen2          vvadia
+askamat               grapacciuolo        ldgraham       rbaheti           vvedanair
+askong                grkulkarni          lecheung       rbasharat         vvsharma
+asmit                 grperlman           ledong         rbertolini        wadawydiak
+asofianopoul          gsantucci           ledwan         rbhal             waluo
+asotocambres          gsbeglia            lee104         rbhansali         wang110
+asoubki               gshivakumar         lee111         rbhowmik          wang113
+asparikh              gshu                lee75          rbiondo           wang132
+asrivastava           gstokes             lehhou         rbird             wang148
+asugumar              gsuczewski          leichen3       rbirnbaum         wang154
+aszekely              gtaylor             leili1         rbodenstein       wang159
+atannenbaum           guayang             leipan         rboseroy          wang54
+ataouil               guayu               leizhou        rbronstein        wang84
+ateklu                guazeng             leprentis      rburgert          wangzhang
+ateplukhin            guffeng             leriksson      rcconley          wawen
+athatikunta           gurpreetsing        lernunez       rchabot           wayou
+athennarasu           guwechue            lessig         rckline           wazzhang
+athonis               gvaillant           lesyan         rcrizzo           wbrett
+atosolini             gverma              letucker       rcsingh           wcun
+atpradhan             gvorobyev           lgruenburg     rdavuluri         wcunningham
+atripoli              gyoun               lhinners       rdefrancisco      wdaniels
+atsegaimoore          gyzhang             lhthorne       rdhaipule         wecui
+atsenthilnat          gzakharov           li1            rdhawan           weibhuang
+atvarghese            gzborovsky          li20           rdhillon          weicdeng
+aubutt                haawilliams         li3            rdogra            weichang
+audupashanka          haenalee            li32           rdrocha           weichang.OLD
+auhhuang              hagguo              liangzhu       rdrucker          weicheng
+avaradarajan          hahkhan             liannchen      rediaz            weihong
+avisingh              haichwang           lichen8        refem             weihsu
+avonalbertin          hailxu              lichiang       relkin            weihwang
+avonderlinde          hakcakaya           lifwang        relyu             weili3
+avpatil               hallu               lihahuang      renunez           weipeng
+avperry               hamorales           lihazhang      rfkelly           weishen
+awalling              hanhan              lihexu         rflood            weishi2
+awardah               hanschoi            lihnguyen      rflorek           weiszhong
+awgriffith            hanxwu              lin56          rfrisina          weitan
+awills                hanzhou1            linchen3       rgadi             weituchen
+awjohnso              haochuwang          lincyu         rgaonkar          weizhu
+aydas                 haolin1             lingjpan       rgautam           welliao
+ayedageresud          haolyu              lingyang       rgiles            wenblu
+ayedlarajaia          haorazhang          linjjiang      rgmillard         wenbwang
+ayendluri             haotxu              linxu          rgonzalez         wendazhang
+ayepuri               haowezheng          linyi          rgzhang           wendhu
+ayreddy               haoyzheng           lirzheng       rhande            wendu
+aysaleem              haraja              liszheng       rharrison         wendyang
+ayshim                harbhatt            liu36          rhelbock          wenhgao
+ayusrivastav          harlee              liu61          rherman           wenjihuang
+aziafat               hasaadi             liuwang        rhesler           wensliu
+azuzow                hasmoon             liuyang2       rhoffren          wentawu
+babrahall             hayyan              liuyzhou       rhua              wequ
+bagarcia              hazhan              liwyang        richatterjee      whiwong
+ballam                hbchao              ljescobar      richkim           wholt
+baminazad             hbien               lkarpuskasan   richlin           wihu
+bangchen              hborchert           lkassetti      rijayaraman       withomas
+bastark               hchawla             lko            rikaur            wiwang
+bavinash              hchenwu             lkrug          rikeh             wixiang
+bbelisle              hdle                llevack        riraquib          wjchen
+bboysan               hdonga              llingda        risjain           wknop
+bbrendan              hduong              lmadiraju      rispatil          wlancer
+bbulag                hechu               lmaeba         ritagarwal        wlian
+bchauhan              heekwon             lmanathungam   riwu              wmichael
+bciranni              henrwang            lmconnolly     rizhuang          woaks
+bclevine              hetariq             lmdeoliveira   rjayaramared      wriggs
+bcolle                hewwang             lmunad         rjbrowne          wsander
+bcuadrado             hhyao               lnazarov       rjdesmond         wsanderson
+bdanna                hipham              lnie           rjeyachandra      wshih
+bdarapu               hjlynch             lnolasco       rjhuang           wsuttle
+bdebarrosfer          hjtrivedi           lonhan         rjleung           wthornton
+bdelamonica           hjudson             lorlowski      rjsoni            wweaver
+bding                 hkaddour            loswanson      rjwillett         wweiqiao
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+bejean                hkhazaei            lparrillamon   rkhatwani         xdmod
+bennliu               hkirby              lpbui          rkhot             xiachu
+benyu                 hle                 lpei           rkidambi          xiamu
+bessuman              hleung              lpintodealme   rkoots            xianaliu
+bewwong               hmainguy            lprowant       rkyatham          xiangyuhuang
+bewwu                 hmdonaldson         lraguette      rlarsen           xiangyyang
+bezzheng              hmoonam             lrastelli      rlpersaud         xiaocao
+bfei                  hmoura              lrole          rlsiford          xiaodliu
+bfeole                hnegi               lsaleh         rmakheja          xiaogli
+bfochtman             hniederhause        lscampbell     rmalga            xiaohawang
+bfogg                 hnnguyen            lschappell     rmandloi          xiaohuliu
+bfutcher              hoannguyen          lschutz        rmangalampal      xiaokzhao
+bglevine              hogao               lshekhar       rmanku            xiaoleyang
+bgoncalves            hokwak              lstrey         rmatsibekker      xiaolhu
+bgourbal              holiver             ltalbot        rmax              xiaolhuang
+bgoyal                honghuang           ltngo          rmenezes          xiaolucheng
+bguruvayoorm          honglliu            ltorpey        rmoffitt          xiaotiawang
+bharrell              honglu              ltorrehealy    rmohan            xiaotoli
+bhkumar               hongwchen           luge           rmudhuganti       xiaoxyang
+bhowlader             hongyuli            lujjia         rmuthu            xiaoysun
+bhshin                honhuang            luoshi         rnarvekar         xiaoyuli
+bhsiao                hotnguyen           lusu           rnorthrup         xiaoyuyang
+bighimire             hppatil             luzou          rochandramoh      xicao
+bihyu                 hqaiser             lvasanthakum   rodtan            xichen10
+binnchen              hranjan             lverma         roessig           xinachen
+binzhou               hridout             lvotapka       rohshukla         xingma
+bishi                 hrmohammed          lwollmuth      romjohnson        xingtzhou
+bisshrestha           hrrajput            lwreid         ronassar          xingyichen
+bji                   hsarkar             lyohe          ronwang           xingywang
+bjkramer              hschang             lyrodrigues    root              xingzguo
+bjlai                 hsekino             maaibrahim     rorosenberg       xinhahuang
+bjlee                 hseyyedzadeh        maalynch       roshukla          xinlu2
+bjnelson              hshafiq             maamandola     roychen1          xinqian
+bjqi                  hsiachang           mabruzzeseot   rparsons          xintang
+bjugan                hsingathala         madambrosio    rpatanwadia       xinwang2
+bkhanikaev            hsirotkin           madkar         rpatro            xinwang5
+bkovarovic            hsnyders            madowling      rpatwary          xinxu4
+blanunez              htalavera           maedelmann     rperna            xinyazheng
+blukacsy              huang54             maescobarrod   rpghosh           xinyin
+bluy                  huaxiao             maggchen       rpmchugh          xiulzhang
+bmahal                huichen5            maggonzalezg   rpohankar         xiwhuang
+bmariano              huideng             maghazahedi    rpopper           xixxiong
+bmchapman             huidliu             magmarkowska   rraghunathan      xizhang1
+bmhenn                huisong             maguevarra     rrani             xji
+bmhyland              huixu1              mahahn         rristowhadli      xjiao
+bmkaufman             huixzhu             mahhasan       rritu             xqliu
+boakley               hullee              mahiralam      rsamulyak         xsha
+bocao                 hungwchen           maiyedun       rsandhu           xshuqian
+bohhuang              huntwale            makhdhor       rsarker           xuaqi
+boisuh                huyzhang            makinboade     rsejour           xuaxu
+borwang               hvannieuwenh        makmalone      rsher             xudeng
+bossun                hvig                makowalchyk    rshilkrot         xuebwang
+bowusufrimpo          hvijayakumar        maksen         rshimogawa        xueqli
+bozhao1               hwoh                maliyari       rsihag            xuxie
+bpamuk                hxing               malvin         rsison            xyuan
+bpilosov              hyejichoi           mamahzabin     rsmolinski        yaagarwal
+bquang                hyemkim             mamandola      rsoori            yakang
+bquang.OLD            hyeocho             mamlan         rspowers          yang28
+brampanellid          hyeonkyung          maochoa        rstusalitus       yang34
+brbartlett            hykoo               mapak          rtamarkin         yangfwu
+brgraham              hymin               mapang         rtelikicherl      yangli10
+brlai                 hyochung            marif          rthacker          yangli9
+brlgonzalez           hyuchung            marioreyes     rtrybulski        yanglu2
+brma                  hyulim              markhangelsk   ruhipatel         yangxie
+brmcgovern            hyunjuncho          markong        ruicxu            yangzhang
+brmoses               hyunsikim           masharma       ruiding           yangzhou
+brpark                hzhan               masong         ruihechen         yanwang2
+brsantos              hzohair             matique        ruiqiwang         yaoli2
+brshao                iabbasparker        matjones       ruishi            yaozou
+brwwang               iakgun              mattchang      rulliu            yashu
+bryang                iakim               mavanalstine   runcli            yaspatel
+brzhou                ialabed             mawwa          ruossun           yaxuan
+brzhu                 ibilkhu             maxmuller      ruparekh          yazadeh
+bsbernstein           ibipul              mazhao         rusharma          yazou
+bschiller             ibolger             mazzimontire   ruyu              ybajaj
+bsen                  ibromberg           mbandham       rwales            ychao
+bshan                 icisternino         mbarbosa       rwilson           yding
+bsheller              ifaridi             mbastan        rxli              yehu
+bsheridan             igkane              mbender        ryachen           yejikim3
+bspitzbart            igrehn              mbianchi       ryanglee          yeke
+bsterling             ihubbard            mbliss         ryao              yellaham
+bsundahl              iinani              mboisvert      rycchan           yenwchen
+btenreiro             ijacob              mbolko         rychin            yenwechen
+btmichalowic          ijhuang             mborczuk       ryengel           yeonskang
+buli                  ikao                mbowen         rygeorge          yhannun
+bvilla                ikotler             mbozok         rysalernoeic      yhasib
+byungjkim             iloop               mbrunger       rzlin             yhochberg
+caaugustine           ilopezcoto          mbuskirk       saachowdhury      yibqi
+caaventura            imarchitelli        mcaponegro     saaikhan          yichuang
+calyu                 inikiforakis        mcfoley        sabedin           yiclin
+camcdonough           iojima              mchio          sabergman         yicozhu
+caponteriver          iosipitan           mcirrito       sabeykoon         yidcheng
+caprea                iouthwaite          mckoch         sabousamra        yifagao
+cargomes              iparaskevako        mclim          saconstantin      yifasun
+carhall               ipjohnson           mcng           sadas             yifewu
+carlliu               ipunn               mconners       sadeshpande       yigao2
+carlopez              iramakrishna        mdabhole       sadsharma         yihanwang
+carty                 ishin               mdarita        saerkim           yihsu
+cballena              isiergiej           mdatar         saffan            yihua
+cbehan                istaylor            mdavariesfah   sagchandrash      yijiang3
+cbetz                 itaradachuk         mdeisler       saichowdhury      yijing
+cblackwell            itrivedi            mdelasaysork   saihaque          yijliu
+cboon                 iurbinahenri        mdhuang        saismail          yijtian
+cbrandon              ivalin              mdovedytis     sakader           yijzhu
+cbudd                 ivanlin             mdsweeney      sakhalifa         yiliu4
+cbunner               ivaratharaja        mdwalam        sakinney          yilma
+ccardetti             iwankavala          meemcnamara    sakotagiri        yimzhao
+ccarew                jaapatel            meijli         samachen          yimzhu
+ccdressler            jabauer             meisanchezpe   samesingh         yingczhou
+ccgordon              jabryan             meisong        samhoque          yingfan
+cchecastaldo          jacacosta           meliasi        samichowdhur      yinglu1
+ccioffi               jaccao              meliot         samrosner         yinou
+ccolosqui             jackili             memendi        samung            yinxzhang
+ccorbo                jacobsmith          mempark        samvasquez        yinyou
+ccpeterson            jacojoseph          menalam        sangyoon          yipli
+cdehury               jacparker           menchowdhury   sarani            yiqguo
+cdehury.OLD           jacsegal            mengao         sasaluja          yittian
+cdelorenzo            jaejeong            mengjliu       sashrestha        yiwasaki
+cdreyer               jaevangelist        menglin1       sasnyder          yiwchao
+cegarrison            jaeyojung           mengrzhang     sastephens        yixcui
+celkhoury             jafinn              mengtliu       sasurana          yiyayu
+cexu                  jafu                mengwu         saswang           yiyizhou
+ceyeung               jagluzman           mengxwang      satsaha           yizholi
+cfeldman              jaharora            mesch          saukumar          yjetwani
+cflagg                jahua               meserranosos   saupaul           ykakade
+cfnapoli              jaimehta            meyasmin       saursingh         ykhaliqui
+cfontanini            jakaczmarzyk        meyue          savargas          ykuyu
+cforan                jakhil              mezaman        saysharma         ymaung
+cgarybicas            jakkatz             mfbugallo      sazchowdhury      ymondal
+cgauthier             jalbanes            mferdman       sbadlia           yneelam
+cgobler               jalbertigles        mfierek        sbaines           yohe
+cgrieco               jalzamoramar        mfirmansyah    sbajjuri          yokato
+cgueli                jamarini            mfite          sbanam            yokee
+cguerraamori          jamoscosonun        mforslund      sbatheja          yoki
+chacho                jange               mfoydl         sbeesabathun      yomma
+chahan                jannguyen           mfucci         sbeg              yongjzhang
+chalpern              janswong            mgarciadiaz    sbenz             yongmchoi
+changhpark            jaschow             mgcortes       sbhuma            yongshin
+changjli              jashukla            mghaderibane   sbillah           yonxiang
+chanzhang             jasjiang            mghogale       sbinnamangal      yoshen
+charwong              jasolau             mgholamianji   sbire             youcha
+chccai                jasonwang           mgivehki       sbirrer           youngkwon
+chdang                jaswsingh           mgwhite        sboddeti          younkang
+chen110               jathoffman          mhanubal       sboppudi          yousshin
+chen147               jaygutierrez        mhare          sbrahmadevar      ypichkar
+chen15                jazpurua            mhaziz         sbscott           yrhamatzada
+chen157               jbak                mhijikata      sburgert          ysingh
+chen175               jbakalis            mhorowitz      scberg            ysoh
+chen181               jbalsamo            mhott          scduppala         yson
+chen182               jbarrantes          miachristie    scentorrino       ysoroka
+chen32                jbarron             miahe          schheda           ytham
+chen77                jbernauer           mianchen       schiappone        yuanjchen
+chencjiang            jbeutel             mibbowman      schook            yuanzhao
+chenclu               jbhambure           michaliang     scokro            yuasong
+chenczhu              jbickel             michelhuang    scsteiger         yuchen4
+chenghli              jbkelly             michellhuang   sdedhia           yuchen7
+chengklin             jbohne              michhuang      sdefaz            yuchzhou
+chengpsun             jbraick             micnicolette   sdescalso         yucma
+chenliang             jbrimlow            micxu          sdhalleweyn       yucpu
+chetheringto          jbrunelle           miczhao        sdisalvo          yucsun
+cheye                 jbuckley            miduan         sdivilov          yucxing
+chezheng              jbuckley.OLD        mignatov       sdsouza           yucye
+chgraham              jburzachiell        mihur          sdssingh          yudding
+chguo                 jcano               mijia          sebramirezvi      yudichen
+chhhogan              jcaputi             mijrivera      seg               yuechen4
+chichiang             jcassella           milobi         seojchang         yuefandeng
+chienlee              jcespedes           miloska        seongan           yuehuang
+chihhchang            jchaillet           mimak          seonghjeong       yuejin
+chihu                 jchivu              minghazhang    seongioh          yuewang6
+chiuyu                jchlee              mingsun        seshin            yuewang7
+chlow                 jcmichel            mingyli        sestoller         yuewlin
+chmorales             jcodere             mingyzhang     seunchoi          yuezhao2
+chodgdon              jcolaizzo           minhwang       sexia             yufchen
+chou                  jcollier            minkwan        sfardeen          yuhajiang
+chriskim              jconesa             miray          sfarhat           yuhwu
+christwong            jdarling            mireza         sfarnan           yulma
+chtian                jdcraig             miswong        sfinch            yuluwang
+chuahuang             jdeneau             mjadhav        sfiola            yulyu
+chugo                 jdesilva            mjavanmard     sfluo             yumichen
+chuntchan             jdovi               mjbonney       sgajjala          yunhxu
+chuzhu                jdscully            mjchun         sgala             yunjeon
+chuzou                jdubnau             mkaltak        sgenovese         yunlzhang
+chyou                 jdwarren            mkamiya        sghavamnia        yunpan
+chyyoon               jecao               mkanasani      sghavat           yupeng
+chzuo                 jefzhong            mkanasani.OLD  sgholami          yuqianwu
+cikang                jegaillard          mkapadia       sghorashi         yuqiao
+ciriccio              jejchan             mkaribian      sgopalan          yushuang
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+cjzheng               jelsoudy            mkishore       sgrao             yuttian
+ckapre                jemak               mkochert       sgrieninger       yuwang7
+ckarwan               jemchen             mkoga          sgurram           yuwzhang
+ckelton               jenfu               mkondeti       sguru             yuxia4
+ckochath              jepace              mkonovalyuk    sgwilliams        yuxlin
+cksullivan            jerlin              mkoraiem       sgyuho            yuxuanzhang
+cleeliang             jeryeung            mkpatel        shaamin           yuxushi
+clegett               jesgoldstein        mkritzer       shakislam         yuxwu
+clfischer             jeslong             mksanda        shalirou          yuyguo
+clongarini            jessewang           mkurakula      shanhe            yuzhwang
+clsears               jettran             mlaul          shanlin2          yyokoi
+cltong                jevalle             mlauterbur     shaoliu           zafahmad
+cltucker              jeyeung             mlcollier      shaowang          zalseika
+cluhmann              jeyyoo              mlng           shaqin            zariahmed
+clwolfe               jfmoon              mlondoo        sharinarayan      zballard
+cmack                 jgaige              mloverde       shawmathew        zbhinderwala
+cmcarey               jgajello            mmadeira       shcchakrabor      zcheslog
+cmcgrew               jgergen             mmahboob       shclay            zcytryn
+cmehndiratta          jglazar             mmahim         shdesai           zdoora
+cmflynn               jglimm              mmaitra        shdixit           zdowling
+cmfoley               jgurevitch          mmakeev        shdixit.OLD       zdupont
+cmjurgensen           jhajagos            mmarder        shechoi           zexizhang
+cmkennedy             jharder             mmaskaliova    shengzhu          zeyao
+cmoczygemba           jheerwig            mmasoumi       shengzwang        zezhu
+cmoote                jheinz              mmatero        shenjin           zfallon
+cmorantesari          jheraghty           mmaung         sheshao           zgrandison
+cmwoo                 jhjung              mmcduffie      shexiong          zgungor
+cnoe                  jhollister          mmcneill       shikgupta         zhacai
+cnoutsos              jhpark              mmerenstein    shilgupta         zhage
+codlam                jiabwang            mmilhaven      shilliu           zhagu
+cohwarner             jiachzhu            mmimurphy      shiltian          zhang100
+cojiang               jiacxu              mmursheed      shitsai           zhang110
+cokeoma               jiahuwang           mniznikiewic   shivansharma      zhang118
+coleary               jiajgao             mnovotny       shivgupta         zhang123
+concao                jiaji               moamin         shiyuawang        zhang133
+conliu                jiakwang            mobusan        shkhalid          zhang142
+cpercival             jialai              moewilliams    shmmohammed       zhang152
+cpethe                jialin1             moflus         shmondal          zhang173
+cpinizzotto           jiamili             mogao          shopatel          zhanyang
+cplizio               jiamwu              mogoel         shperalta         zhaoliu
+cprasad               jianfeng            mohassan       shrajput          zhchai
+cqiu                  jianflin            mojia          shroy             zhddong
+cradke                jianhan             molssi000      shrraman          zhedzhang
+crcollinswor          jianjliu            molssi001      shsaha            zhefang
+crfernandesv          jianmtan            molssi002      shshekhar         zheng13
+csangiovanni          jiannyang           molssi003      shshekhar.OLD     zheng30
+csantoni              jianxiozhang        molssi004      shsin             zhengxwang
+csasmith              jiaojiang           molssi005      shssridhar        zhenjhuang
+cschwaner             jiapatel            molssi006      shtao             zhenliu
+cshiveshwark          jiasu               molssi007      shuaguo           zhenlu
+csiebor               jiatian             molssi008      shubwang          zhenqian
+csimmerling           jiawang1            molssi009      shuhe             zhenwu
+csingleton            jiaweichen          molssi010      shujia            zhenxliu
+cstussman             jiawezhu            molssi011      shyyoo            zheychen
+csyreilly             jiaxuyu             molssi012      shyyuan           zhezhou1
+cthakur               jiayeguo            molssi013      shzzhou           zhibwang
+ctinker               jiayyan             molssi014      siasun            zhibyang
+ctustin               jibbai              molssi015      sichchen          zhideng
+cuwang                jichao              molssi016      sicheliu          zhihhe
+cvorkas               jiddong             molssi017      sichhabra         zhihhuang
+cweistuch             jiechen3            molssi018      sichliu           zhijli
+cwoellhof             jiemchen            molssi019      sigadkar          zhimalin
+cxi                   jiemzeng            molssi020      siggupta          zhipxu
+cyanagisawa           jienzhu             molssi021      sihqian           zhiwlin
+cyluo                 jieyang             molssi022      sijhuang          zhixzhang
+cyoungflesh           jihlin              molssi023      sijjiang          zhiye
+czhen                 jihoopark           molssi024      sijliu            zhke
+d9wang                jihuynh             molssi025      silai             zhlee
+dabelinsky            jihyepark           molssi026      singanne          zhonliang
+dagolden              jiikim              molssi027      singh4            zhouyu1
+dagrange              jijin               molssi028      sinhong           zhuhli
+daiwang               jilao               molssi029      sinlin            zhuxie
+dalpancakmak          jiliu1              molssi030      sinsmith          zhwong
+damcintyre            jimlin              molssi031      sirle             zhxia
+damiruddin            jimun               molssi032      sishizawa         zidiao
+damoses               jin                 molssi033      siskhakov         ziguan
+dandrew               jinghzhou           molssi034      siuchan           zijiao
+dangelidis            jingwenli           molssi035      siwewang          zijizhou
+danieliang            jingwezhang         molssi036      sixliu            zikhan
+danitorresra          jingwliu            molssi037      siyadav           zilinchen
+danizheng             jinkokim            molssi038      siyao             zilwu
+dantorres             jinwang2            molssi039      siyimaya          zirliu
+dantyu                jinwei              morahimi       siyzou            zishao
+danwei                jinyhu              moriasaranib   sizahid           ziweiwang
+daoconnell            jinyinwang          mozhao         sizzheng          ziwyu
+dappark               jinyli              mperess        sjaffary          zixli
+darkow                jinyuyang           mpersch        sjamshad          ziyli
+darlin                jinyxu              mpetrusky      sjeevan           ziyozhang
+darvind               jinzwang            mpkatz         sjens             ziyye
+darzeng               jiqian              mpsantomauro   sjiecheng         zkrayem
+dathanasakos          jiychong            mquispecarba   sjnelson          zlyu
+daultmccoy            jiyim               mradfar        sjyang            zmou
+davidlin              jiyjung             mrahimibolda   skade             zniu
+davizhao              jiyounpark          mrakhar        skagana           zoanderson
+davliang              jiyuliu             mrashid        skalam            zoxie
+davsilverman          jiyuyang            mrathore       skalva            zqiao
+dawan                 jjcarter            mrayeesuddin   skann             zsongzhu
+dawei                 jjguo               mrehan         skapse            zuzheng
+dawendt               jjjones             mreuter        skapur            zwray
+dawhu                 jjnielsen           mrichter       skarnik           zye
+daxxie                jkable              mrius          skatariya         zzaidi
+dayeung               jkiryluk            mrkumar        skavuri           zzhuang
+dayyan                jkodner             mrosati        sketchum          zzoya
+dayyoon               jkohara             mrsun          skobayashi
+dbasu                 jkonopka            msardis        skogilathota
+(base) [ehspector@milan1 home]$ cd ..
+(base) [ehspector@milan1 gpfs]$ cd projects/AMS536
+(base) [ehspector@milan1 AMS536]$ ls
+  2019  2021  2023  2025            junk.txt     zzz.programs
+  2020  2022  2024  get_anchors.py  zzz.anchors
+(base) [ehspector@milan1 AMS536]$ cd zzz.programs/
+(base) [ehspector@milan1 zzz.programs]$ ls
+amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
+de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
+dock6.10         dock6.12         gen-frags-12         VS_libraries
+dock6.10_milan   dock6.12_ams536  old
+(base) [ehspector@milan1 zzz.programs]$ cd dock6.12_ams536/
+(base) [ehspector@milan1 dock6.12_ams536]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@milan1 dock6.12_ams536]$ cd parameters/
+(base) [ehspector@milan1 parameters]$ ls
+                         fraglib_linker.mol2         prot.table.ambcrg.sybH
+antechamber               fraglib_scaffold.mol2       sa_fraglib.dat
+chem.defn                 fraglib_sidechain.mol2      screen.in
+chemgrid                  fraglib_torenv.dat          screen.para
+chem_match.tbl            leap                        vdw_AMBER_parm94.defn
+flex.defn                 na.table.ambcrg             vdw_AMBER_parm94.dock3_7.defn
+flex_drive_mod.tbl        pains_table_2019_09_01.dat  vdw_AMBER_parm94.dock3_7_one_C_3.defn
+flex_drive.tbl            pains_table.dat             vdw_AMBER_parm96.defn
+flex_just_OH.defn         ph4.defn                    vdw_AMBER_parm99.defn
+flex_mod2.defn            prot.table.ambcrg.ambH      vdw_de_novo.defn
+flex_mod.defn             prot.table.ambcrg.pdb3H     vdw.parms.amb
+fraglib_ga_scaffold.mol2  prot.table.ambcrg.pdbH      vdw.parms.update.amb
+(base) [ehspector@milan1 parameters]$ pwd
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters
+(base) [ehspector@milan1 parameters]$ class
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/004_energymin/
+(base) [ehspector@milan1 004_energymin]$ vi min.in
+(base) [ehspector@milan1 004_energymin]$ touch max.in
+(base) [ehspector@milan1 004_energymin]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/
+(base) [ehspector@milan1 dock6.12_ams536]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@milan1 dock6.12_ams536]$ cd bin/
+(base) [ehspector@milan1 bin]$ ls
+am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
+amberize_complex   espgen        nchemgrid_GB          showbox
+amberize_ligand    grid          nchemgrid_SA          showsphere
+amberize_receptor  grid-convert  parmcal               solvgrid
+antechamber        grid-convrds  parmchk               solvmap
+atomtype           make_phimap   prepare_amber.pl      sphere_selector
+bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
+chemgrid           mol2.py       prepgen               teLeap
+combine_torenv.py  mopac         resp                  tleap
+dock6              mopac.sh      respgen
+(base) [ehspector@milan1 bin]$ pwd
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
+(base) [ehspector@milan1 bin]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/
+(base) [ehspector@milan1 5EEN]$ cd 004_energymin/
+(base) [ehspector@milan1 004_energymin]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i max.in
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+                                             ligand_atom_file [database.mol2] ():../001.structure/2ITO_ligand_Gefitinib_final.mol2
+                                            limit_max_ligands [no] (yes no):
+                                                skip_molecule [no] (yes no):
+                                           read_mol_solvation [no] (yes no):
+                                               calculate_rmsd [no] (yes no):yes
+                                       use_rmsd_reference_mol [no] (yes no):yes
+                                      rmsd_reference_filename [ligand_rmsd.mol2] ():../001.structure/2ITO_ligand_Gefitinib_final.mol2
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):
+                                     grid_score_rep_rad_scale [1] ():
+                                         grid_score_vdw_scale [1] ():
+                                          grid_score_es_scale [1] ():
+                                          grid_lig_efficiency [no] (yes no):
+                                       grid_score_grid_prefix [grid] ():../003_gridbox/grid
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+                                              minimize_ligand [yes] (yes no):
+                                       simplex_max_iterations [1000] ():
+                               simplex_tors_premin_iterations [0] ():
+                                           simplex_max_cycles [1] ():
+                                       simplex_score_converge [0.1] ():
+                                       simplex_cycle_converge [1.0] ():
+                                           simplex_trans_step [1.0] ():
+                                             simplex_rot_step [0.1] ():
+                                            simplex_tors_step [10.0] ():
+                                            simplex_final_min [no] (yes no):
+                                          simplex_random_seed [0] ():
+                                        simplex_restraint_min [no] (yes no):yes
+                                simplex_coefficient_restraint [10.0] ():
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+                                                   atom_model [all] (all | united):
+                                                vdw_defn_file [vdw.defn] ():
+                                               flex_defn_file [flex.defn] ():
+                                              flex_drive_file [flex_drive.tbl] ():
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+                                        ligand_outfile_prefix [output] ():
+                                          write_mol_solvation [no] (yes no):
+                                           write_orientations [no] (yes no):
+                                        num_scored_conformers [1] ():
+                                              score_threshold [100.0] ():
+                                                 rank_ligands [no] (yes no):
+------------------------------------------------------------------------------------------
+Could not open vdw.defn for reading.  Program will terminate.
+(base) [ehspector@milan1 004_energymin]$ vimdiff min.in max.in
+files to edit
+(base) [ehspector@milan1 004_energymin]$ rm max.in
+(base) [ehspector@milan1 004_energymin]$ vi min.sh
+(base) [ehspector@milan1 004_energymin]$ vi min.in
+(base) [ehspector@milan1 004_energymin]$ bash min.sh
+(base) [ehspector@milan1 004_energymin]$ ls
+een.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan1 004_energymin]$ vi min.out
+(base) [ehspector@milan1 004_energymin]$ ls
+een.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan1 004_energymin]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ ls
+  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ mv 1086/ 1O86
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 1O86/commands.txt
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ ls
+commands.txt
+(base) [ehspector@milan2 1O86]$ bash commands.txt
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
+  [Bookmarked Feb 7, 2025 at 3:22:42 PM]
+(base) [ehspector@milan2 1O86]$ mv 004_dock/ 004_energymin
+(base) [ehspector@milan2 1O86]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+(base) [ehspector@milan2 001_structure]$ ls
+O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
+O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+O86_surface.dms
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 5EEN]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+een.sph  5een_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/sphere.sph 1O86/002_surface_spheres/sphere.sph
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 1O86/002_surface_spheres/select.sph
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/INSPH 1O86/002_surface_spheres/INSPH
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+O86_surface.dms  INSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+At line 131 of file sphgen.f (unit = 4)
+Fortran runtime error: Cannot open file '5een_surface.dms': No such file or directory
+Error termination. Backtrace:
+#0  0x7ffff7d54ca5 in already_open
+	at ../../../libgfortran/io/open.c:742
+#1  0x404f73 in ???
+#2  0x40117c in ???
+#3  0x7ffff742958f in ???
+#4  0x7ffff742963f in ???
+#5  0x4011b4 in ???
+#6  0xffffffffffffffff in ???
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+At line 125 of file sphgen.f (unit = 6)
+Fortran runtime error: Cannot open file 'OUTSPH': File exists
+Error termination. Backtrace:
+#0  0x7ffff7d54ca5 in already_open
+	at ../../../libgfortran/io/open.c:742
+#1  0x404e9e in ???
+#2  0x40117c in ???
+#3  0x7ffff742958f in ???
+#4  0x7ffff742963f in ???
+#5  0x4011b4 in ???
+#6  0xffffffffffffffff in ???
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+At line 125 of file sphgen.f (unit = 6)
+Fortran runtime error: Cannot open file 'OUTSPH': File exists
+Error termination. Backtrace:
+#0  0x7ffff7d54ca5 in already_open
+	at ../../../libgfortran/io/open.c:742
+#1  0x404e9e in ???
+#2  0x40117c in ???
+#3  0x7ffff742958f in ???
+#4  0x7ffff742963f in ???
+#5  0x4011b4 in ???
+#6  0xffffffffffffffff in ???
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+At line 125 of file sphgen.f (unit = 6)
+Fortran runtime error: Cannot open file 'OUTSPH': File exists
+Error termination. Backtrace:
+#0  0x7ffff7d54ca5 in already_open
+	at ../../../libgfortran/io/open.c:742
+#1  0x404e9e in ???
+#2  0x40117c in ???
+#3  0x7ffff742958f in ???
+#4  0x7ffff742963f in ???
+#5  0x4011b4 in ???
+#6  0xffffffffffffffff in ???
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi 1086_new_surface.dms
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86_surface.dms  INSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86.sph  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86.sph  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 1O86]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
+O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
+(base) [ehspector@milan2 001_structure]$ ls
+O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
+O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ bash select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86_surface.dms  OUTSPH                select.sph
+O86.sph              INSPH             selected_spheres.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+_new_surface.dms  1O86_surface.dms  OUTSPH                select.sph
+O86.sph              INSPH             selected_spheres.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.sh 1O86/003_gridbox/showbox.sh
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.in 1O86/003_gridbox/showbox.in
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ bash showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+O86.box.pdb   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.sh 1O86/003_gridbox/grid.sh
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.in 1O86/003_gridbox/grid.in
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+O86.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
+O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+O86.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.out
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+O86.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
+ grid.bmp       grid.nrg   grid.sh   '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 1O86/004_energymin/min.sh
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 1O86/004_energymin/min.in
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/004_energymin/
+(base) [ehspector@milan2 004_energymin]$ vi min.in
+(base) [ehspector@milan2 004_energymin]$ cd ../001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
+O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
+(base) [ehspector@milan2 001_structure]$ cd ../004_energymin/
+(base) [ehspector@milan2 004_energymin]$ ls
+min.in  min.sh
+(base) [ehspector@milan2 004_energymin]$ bash min.sh
+(base) [ehspector@milan2 004_energymin]$ ls
+O86.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan2 004_energymin]$ vi min.out
+(base) [ehspector@milan2 004_energymin]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 2w26]$ cd 001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+(base) [ehspector@milan2 001_structure]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_surface.dms  INSPH  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+At line 328 of file sphgen.f
+Fortran runtime error: Bad value during floating point read
+Error termination. Backtrace:
+#0  0x7ffff7d59e39 in formatted_transfer_scalar_read
+	at ../../../libgfortran/io/transfer.c:1790
+#1  0x7ffff7d5b535 in formatted_transfer
+	at ../../../libgfortran/io/transfer.c:2491
+#2  0x4049e0 in ???
+#3  0x40516a in ???
+#4  0x40117c in ???
+#5  0x7ffff742958f in ???
+#6  0x7ffff742963f in ???
+#7  0x4011b4 in ???
+#8  0xffffffffffffffff in ???
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_surface.dms
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_surface.dms  INSPH  OUTSPH  sphere.sph  temp1.ms  temp3.atc
+(base) [ehspector@milan2 002_surface_spheres]$ rm temp1.ms
+(base) [ehspector@milan2 002_surface_spheres]$ rm temp3.atc
+(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26_surface.dms  INSPH  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
+(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26.sph  2w26_surface.dms  INSPH  OUTSPH  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 2w26/002_surface_spheres/select.sph
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26.sph  2w26_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ../001_structure/
+(base) [ehspector@milan2 001_structure]$ ls
+w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
+w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
+(base) [ehspector@milan2 001_structure]$ cd ../002_surface_spheres/
+(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ bash select.sph
+(base) [ehspector@milan2 002_surface_spheres]$ ls
+w26.sph  2w26_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
+(base) [ehspector@milan2 002_surface_spheres]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd 003_gridbox/
+(base) [ehspector@milan2 003_gridbox]$ ls
+ grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ rm '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ ls
+grid.in  grid.sh  showbox.in  showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
+(base) [ehspector@milan2 003_gridbox]$ bash showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+w26.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ vi grid.in
+(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
+(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
+(base) [ehspector@milan2 003_gridbox]$ ls
+w26.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
+ grid.bmp       grid.nrg   grid.sh   '&showbox.log&'
+(base) [ehspector@milan2 003_gridbox]$ vi grid.out
+(base) [ehspector@milan2 003_gridbox]$ cd ..
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 2w26]$ vi commands.txt
+(base) [ehspector@milan2 2w26]$ mv 004_dock/ 004_energymin
+(base) [ehspector@milan2 2w26]$ cd 004_energymin/
+(base) [ehspector@milan2 004_energymin]$ ls
+(base) [ehspector@milan2 004_energymin]$ ls
+(base) [ehspector@milan2 004_energymin]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 2w26/004_energymin/min.in
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/004_energymin/
+(base) [ehspector@milan2 004_energymin]$ vi min.in
+(base) [ehspector@milan2 004_energymin]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 2w26/004_energymin/min.sh
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan2 2w26]$ cd 004_energymin/
+(base) [ehspector@milan2 004_energymin]$ vi min.sh
+(base) [ehspector@milan2 004_energymin]$ bash min.sh
+(base) [ehspector@milan2 004_energymin]$ ls
+w26.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan2 004_energymin]$ vi min.out
+(base) [ehspector@milan2 004_energymin]$ client_loop: send disconnect: Broken pipe
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een.sph  5een_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan1 002_surface_spheres]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ home
+(base) [ehspector@milan1 espector]$ cd 4s0v/
+(base) [ehspector@milan1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas_2.in   gas_3.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+gas_2.out  gas.in     no_charge            no_gas.out_scored.mol2
+gas_3.in   gas.out    no_gas.in            test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
+(base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@milan1 gas_teiger]$ ls
+gas_2.in   gas_3.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+gas_2.out  gas.in     no_charge            no_gas.out_scored.mol2
+gas_3.in   gas.out    no_gas.in            test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas_2.out
+(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
+(base) [ehspector@milan1 gas_teiger]$ vi test_mol2
+(base) [ehspector@milan1 gas_teiger]$ vi test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2
+(base) [ehspector@milan1 gas_teiger]$ cd ../../builds/alpha_branch/src/dock
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ home
+(base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@milan1 gas_teiger]$ pwd
+/gpfs/projects/rizzo/espector/4s0v/gas_teiger
+(base) [ehspector@milan1 gas_teiger]$ cp gas_2.in gas_4.in
+(base) [ehspector@milan1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_2.out  gas_4.in  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+AAQ_yesG.mol2  gas_3.in   gas.in    no_charge            no_gas.out_scored.mol2
+gas_2.in        gas_3.out  gas.out   no_gas.in            test.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
+(base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
+(base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ vi gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/
+(base) [ehspector@milan1 5EEN]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
+(base) [ehspector@milan1 002_surface_spheres]$ ls
+een.sph  5een_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
+(base) [ehspector@milan1 002_surface_spheres]$ vi select.sph
+(base) [ehspector@milan1 002_surface_spheres]$ home
+(base) [ehspector@milan1 espector]$ cd ..
+(base) [ehspector@milan1 rizzo]$ home
+(base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@milan1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_2.out  gas_4.in   gas.out              no_gas.in               test.mol2
+AAQ_yesG.mol2  gas_3.in   gas_4.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+gas_2.in        gas_3.out  gas.in     no_charge            no_gas.out_scored.mol2
+(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ rm gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ vi gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_2.out  gas_4.in   gas.out              no_gas.in               test.mol2
+AAQ_yesG.mol2  gas_3.in   gas_4.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
+gas_2.in        gas_3.out  gas.in     no_charge            no_gas.out_scored.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
+(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_2.out  gas_4.in               gas.in               no_charge   no_gas.out_scored.mol2
+AAQ_yesG.mol2  gas_3.in   gas_4.out              gas.out              no_gas.in   test.mol2
+gas_2.in        gas_3.out  gas_4.out_scored.mol2  gas.out_scored.mol2  no_gas.out  test_nocharge.mol2
+(base) [ehspector@milan1 gas_teiger]$ vi gas_4.out_scored.mol2
+(base) [ehspector@milan1 gas_teiger]$ cp gas_4.in gas_5.in
+(base) [ehspector@milan1 gas_teiger]$ vi gas_5.in
+(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_5.in -o gas_5.out
+(base) [ehspector@milan1 gas_teiger]$ vi gas_5.out
+(base) [ehspector@milan1 gas_teiger]$ home
+(base) [ehspector@milan1 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi rdtyper.cpp
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ cd ..
+(base) [ehspector@milan1 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@milan1 src]$ cd dock
+(base) [ehspector@milan1 dock]$ ls
+amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
+amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
+amber_typer.o       fingerprint.h         nab                   score_internal.o
+base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
+base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
+base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
+base_mpi.cpp        fraggraph.o           orient.h              score.o
+base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
+base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
+base_score.cpp      fragment.o            rddrive.h             score_ph4.o
+base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
+base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
+conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
+conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
+conf_gen_ag.o       grid.h                README                score_solvent.h
+conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
+conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
+conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
+conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
+conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
+conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
+conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
+conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
+conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
+conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
+conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
+conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
+conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
+conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
+conf_gen_hdb.o      lol                   score_footprint.h     trace.o
+defreal.h           Makefile              score_footprint.o     utils.cpp
+dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
+dockmol.cpp         master_conf.h         score_gist.h          utils.o
+dockmol.h           master_conf.o         score_gist.o          version.h
+dockmol.o           master_score.cpp      score.h               xlogp.cpp
+dock.o              master_score.h        score_hbond.cpp       xlogp.h
+filter.cpp          master_score.o        score_hbond.h
+filter.h            mem_info.cpp          score_hbond.o
+(base) [ehspector@milan1 dock]$ cd ..
+(base) [ehspector@milan1 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@milan1 src]$ cd ..
+(base) [ehspector@milan1 alpha_branch]$ ks
+-bash: ks: command not found
+(base) [ehspector@milan1 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@milan1 alpha_branch]$ cd src/
+(base) [ehspector@milan1 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@milan1 src]$ cd ..
+(base) [ehspector@milan1 alpha_branch]$ cd install/
+(base) [ehspector@milan1 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@milan1 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 10 01:24:01 PM EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fingerprint.h:13,
+                 from fingerprint.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fingerprint.h:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fraggraph.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fraggraph.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fragment.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from gasteiger.h:8,
+                 from gasteiger.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from gasteiger.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from hungarian.h:7,
+                 from hungarian.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from hungarian.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from library_file.h:9,
+                 from library_file.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from library_file.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from limit_max_change.h:12,
+                 from limit_max_change.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from limit_max_change.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from master_conf.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from master_conf.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from master_score.cpp:2:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from master_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+^Cmake[1]: *** [../../install/rules.h:36: master_score.o] Interrupt
+make: *** [Makefile:28: dock] Interrupt
+(base) [ehspector@milan1 install]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 10 13:29:04 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+^Cmake[1]: *** [conf_gen_ag.o] Interrupt
+make: *** [dock] Interrupt
+(base) [ehspector@login2 install]$ rdkit
+bash: rdkit: command not found...
+(base) [ehspector@login2 install]$ rd
+srun: error: invalid partition specified: short-40core
+srun: error: Unable to allocate resources: Invalid partition name specified
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ rd
+srun: job 925032 queued and waiting for resources
+srun: job 925032 has been allocated resources
+(base) [ehspector@dn018 ~]$ home
+(base) [ehspector@dn018 espector]$ cd builds/alpha_branch/install/
+(base) [ehspector@dn018 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn018 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 10 13:31:12 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fingerprint.h:13,
+                 from fingerprint.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fingerprint.h:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fraggraph.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fraggraph.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fragment.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from gasteiger.h:8,
+                 from gasteiger.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from gasteiger.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from hungarian.h:7,
+                 from hungarian.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from hungarian.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from library_file.h:9,
+                 from library_file.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from library_file.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from limit_max_change.h:12,
+                 from limit_max_change.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from limit_max_change.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from master_conf.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from master_conf.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from master_score.cpp:2:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from master_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from orient.h:7,
+                 from orient.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from orient.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from sasa.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from sasa.h:14:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_amber.cpp:66:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_amber.cpp:55:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_chemgrid.cpp:39:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_chemgrid.cpp:38:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_descriptor.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_descriptor.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_footprint.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_footprint.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_ph4.h:7,
+                 from score_ph4.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_ph4.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_volume.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_volume.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_gist.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_gist.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_hbond.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_hbond.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_internal.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_internal.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_multigrid.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_multigrid.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_sasa.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_sasa.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_solvent.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_solvent.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from simplex.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from simplex.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from utils.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from utils.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.h:12,
+                 from iso_align.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fragment.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
+                 from rdtyper.cpp:18:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from rdtyper.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from rddrive.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from dockmol.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+cd nab && make all
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
+mv dock6.rdkit ../../bin
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Mon Feb 10 13:34:18 EST 2025.
+(base) [ehspector@dn018 install]$ exit
+exit
+(base) [ehspector@milan1 ~]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ home
+(base) [ehspector@milan1 espector]$ cd ..
+(base) [ehspector@milan1 rizzo]$ module load git
+(base) [ehspector@milan1 rizzo]$ home
+(base) [ehspector@milan1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan1 espector]$ git status
+fatal: not a git repository (or any parent up to mount point /)
+Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
+(base) [ehspector@milan1 espector]$ cd builds/
+(base) [ehspector@milan1 builds]$ cd alpha_branch/
+(base) [ehspector@milan1 alpha_branch]$ git status
+On branch alpha_branch
+Your branch is up to date with 'origin/alpha_branch'.
+Changes not staged for commit:
+  (use "git add <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+	modified:   docs/new_in_6.13.txt
+	modified:   src/dock/filter.cpp
+Untracked files:
+  (use "git add <file>..." to include in what will be committed)
+	src/dock/lol
+	src/rdkit/boost/
+	src/rdkit/boost_1_71_0.tar.gz
+	src/rdkit/boost_1_71_0/
+	src/rdkit/eigen-3.3.9.tar.gz
+	src/rdkit/eigen-3.3.9/
+	src/rdkit/rdkit-Release_2019_09_1.tar.gz
+	src/rdkit/rdkit-Release_2019_09_1/
+no changes added to commit (use "git add" and/or "git commit -a")
+(base) [ehspector@milan1 alpha_branch]$ git commit src/dock/filter.cpp
+Aborting commit due to empty commit message.
+(base) [ehspector@milan1 alpha_branch]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 005_virtual_screen/
+(base) [ehspector@milan1 005_virtual_screen]$ ls
+(base) [ehspector@milan1 005_virtual_screen]$ cd ..
+(base) [ehspector@milan1 2w26]$ mv 005_virtual_screen/ 005_footprint/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_footprint           007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 005_footprint/
+(base) [ehspector@milan1 005_footprint]$ ls
+(base) [ehspector@milan1 005_footprint]$ touch footprint.in
+(base) [ehspector@milan1 005_footprint]$ ls
+footprint.in
+(base) [ehspector@milan1 005_footprint]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd 004_energymin/
+(base) [ehspector@milan1 004_energymin]$ ls
+w26.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan1 004_energymin]$ vi 2w26.lig.min_scored.mol2
+(base) [ehspector@milan1 004_energymin]$ ls
+w26.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan1 004_energymin]$ vi min.s
+(base) [ehspector@milan1 004_energymin]$ vi min.sh
+(base) [ehspector@milan1 004_energymin]$ cd ../
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_footprint           007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ vi commands.txt
+(base) [ehspector@milan1 2w26]$ cd ,,
+-bash: cd: ,,: No such file or directory
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_footprint           007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 005_footprint/
+(base) [ehspector@milan1 005_footprint]$ ls
+footprint.in
+(base) [ehspector@milan1 005_footprint]$ mv footprint.in rigid.in
+(base) [ehspector@milan1 005_footprint]$ vi rigid.sh
+(base) [ehspector@milan1 005_footprint]$ cd ..
+(base) [ehspector@milan1 2w26]$ mv 005_footprint/ 005_rigid
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_rigid               007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 005_rigid/
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid.in  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ bash rigid.
+bash: rigid.: No such file or directory
+(base) [ehspector@milan1 005_rigid]$ bash rigid.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+                                             ligand_atom_file [database.mol2] ():
+                                            limit_max_ligands [no] (yes no):
+                                                skip_molecule [no] (yes no):
+                                           read_mol_solvation [no] (yes no):
+                                               calculate_rmsd [no] (yes no):
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):
+                                           automated_matching [yes] (yes no):
+                                           receptor_site_file [receptor.sph] ():
+                                             max_orientations [1000] ():
+                                              critical_points [no] (yes no):
+                                            chemical_matching [no] (yes no):
+                                           use_ligand_spheres [no] (yes no):
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):
+                                     grid_score_rep_rad_scale [1] ():
+                                         grid_score_vdw_scale [1] ():
+                                          grid_score_es_scale [1] ():
+                                          grid_lig_efficiency [no] (yes no):
+                                       grid_score_grid_prefix [grid] ():
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+                                              minimize_ligand [yes] (yes no):
+                                       simplex_max_iterations [1000] ():
+                               simplex_tors_premin_iterations [0] ():
+                                           simplex_max_cycles [1] ():
+                                       simplex_score_converge [0.1] ():
+                                       simplex_cycle_converge [1.0] ():
+                                           simplex_trans_step [1.0] ():
+                                             simplex_rot_step [0.1] ():
+                                            simplex_tors_step [10.0] ():
+                                            simplex_final_min [no] (yes no):
+                                          simplex_random_seed [0] ():
+                                        simplex_restraint_min [no] (yes no):
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+                                                   atom_model [all] (all | united):
+                                                vdw_defn_file [vdw.defn] ():
+                                               flex_defn_file [flex.defn] ():
+                                              flex_drive_file [flex_drive.tbl] ():
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+                                        ligand_outfile_prefix [output] ():
+                                          write_mol_solvation [no] (yes no):
+                                           write_orientations [no] (yes no):
+                                        num_scored_conformers [1] ():
+                                              score_threshold [100.0] ():
+                                                 rank_ligands [no] (yes no):
+------------------------------------------------------------------------------------------
+Could not open vdw.defn for reading.  Program will terminate.
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ rm rigid.in
+(base) [ehspector@milan1 005_rigid]$ touch rigid.in
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid.in  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ bash rigid.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+                                             ligand_atom_file [database.mol2] ():2w26.lig.min.mol2
+                                            limit_max_ligands [no] (yes no):
+                                                skip_molecule [no] (yes no):
+                                           read_mol_solvation [no] (yes no):
+                                               calculate_rmsd [no] (yes no):yes
+                                       use_rmsd_reference_mol [no] (yes no):yes
+                                      rmsd_reference_filename [ligand_rmsd.mol2] ():2w26.lig.min.mol2
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):
+                                           automated_matching [yes] (yes no):
+                                           receptor_site_file [receptor.sph] ():../002_surface_spheres/selected_spheres.sph
+                                             max_orientations [1000] ():
+                                              critical_points [no] (yes no):
+                                            chemical_matching [no] (yes no):
+                                           use_ligand_spheres [no] (yes no):
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):
+                                     grid_score_rep_rad_scale [1] ():
+                                         grid_score_vdw_scale [1] ():
+                                          grid_score_es_scale [1] ():
+                                          grid_lig_efficiency [no] (yes no):
+                                       grid_score_grid_prefix [grid] ():../003_gridbox/grid
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+                                              minimize_ligand [yes] (yes no):
+                                       simplex_max_iterations [1000] ():
+                               simplex_tors_premin_iterations [0] ():
+                                           simplex_max_cycles [1] ():
+                                       simplex_score_converge [0.1] ():
+                                       simplex_cycle_converge [1.0] ():
+                                           simplex_trans_step [1.0] ():
+                                             simplex_rot_step [0.1] ():
+                                            simplex_tors_step [10.0] ():
+                                            simplex_final_min [no] (yes no):
+                                          simplex_random_seed [0] ():
+                                        simplex_restraint_min [no] (yes no):
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+                                                   atom_model [all] (all | united):
+                                                vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_AMBER_parm99.defn
+                                               flex_defn_file [flex.defn] ():
+                                              flex_drive_file [flex_drive.tbl] ():
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+                                        ligand_outfile_prefix [output] ():rigid.out
+                                          write_mol_solvation [no] (yes no):
+                                           write_orientations [no] (yes no):
+                                        num_scored_conformers [1] ():
+                                              score_threshold [100.0] ():
+                                                 rank_ligands [no] (yes no):
+------------------------------------------------------------------------------------------
+Could not open flex.defn for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+Could not open flex_drive.tbl for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Initializing Library File Routines...
+Could not open 2w26.lig.min.mol2 for reading.  Program will terminate.
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ cp rigid.sh rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out
+(base) [ehspector@milan1 005_rigid]$ cd ../004_energymin/
+(base) [ehspector@milan1 004_energymin]$ ls
+w26.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan1 004_energymin]$ cd ../005_rigid/
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.out_scored.mol2  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.out_scored.mol2  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
+(base) [ehspector@milan1 005_rigid]$ cd ..
+(base) [ehspector@milan1 2w26]$ mv 006_virtual_screen_mpi/ 006_flex_docking
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_rigid         007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_flex_docking  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 005_rigid/
+(base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_rigid         007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_flex_docking  008_rescore        Notes.txt
+(base) [ehspector@milan1 2w26]$ cd 001_structure
+(base) [ehspector@milan1 001_structure]$ ls
+w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
+w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd 005_rigid/
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.out_scored.mol2  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
+(base) [ehspector@milan1 005_rigid]$ vi rigid.out
+(base) [ehspector@milan1 005_rigid]$ vi rigid.in
+(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
+(base) [ehspector@milan1 005_rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.out_conformers.mol2  rigid.out_scored.mol2  rigid.sh
+(base) [ehspector@milan1 005_rigid]$ grep -c "Name" rigid.out_scored.mol2
+(base) [ehspector@milan1 005_rigid]$ client_loop: send disconnect: Broken pipe
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan1 ~]$ cd AMS_536/
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd ..
+(base) [ehspector@milan1 ~]$ cd ..
+(base) [ehspector@milan1 home]$ ls
+caaachase              dbobo               jksullivan     msazonova         skorada
+aaaggarwal            dcalabria           jktsui         mschedel          skotelnikov
+aaaggarwal.26FEB2020  dcazorla            jleehand       mschrimpf         skotla
+aabdurrob             dcbrown             jlfong         mschwaller        skrichevsky
+aabhilash             dcharan             jlguerra       mshaaban          skristam
+aadarsh               dchien              jlipshultz     mshahneousba      skrupp
+aadubois              ddassanis           jlomanto       mshih             sladerwager
+aagashe               ddelayo             jluceno        mshinder          slakshminara
+aagishtein            ddemartini          jlungu         mshu              slaverty
+aahern                ddukes              jlutsky        msilfies          slthomas
+aaiyer                deachen             jlweissman     msmoawad          smadishetty
+aajith                decarlson           jmaghakian     msrao             smaiti
+aakale                dekblom             jmarcantonio   msreeves          smallipattu
+aakiti                delam               jmarciano      mstanacevic       smamalis
+aakkumar              demccabe            jmayortorres   msweber           smartynenko
+aaksenova             dereliu             jmeliker       mtalukder         smascarenhas
+aaliang               deroy               jmendezmende   mthu              smconnors
+aallin                devlin              jmgentile      mtoledorozyc      smdick
+aallu                 dfarahmandpo        jmiao          mtsonev           smedved
+aalpern               dfei                jmitchell      mturk             smeghdadizan
+aamahmood             dfucich             jmorkos        mumarani          smelhiraj
+aambrown              dgaidhani           jmulackal      muprit            smesiha
+aamgalan              dgenet              jmurrugarral   mvalakonda        smhenry
+aaminev               dgersappe           jmurzaku       mvashishtha       smiduthuri
+aamurthy              dg-mgmt1-auth-keys  jmvasquez      mvfernandezs      smilakovic
+aanaggarwal           dg-mgmt2-auth-keys  jnassar        mvilensky         smirghafouri
+aanagnostopo          dgnatenko           jnatarajan     mwilking          smirroshande
+aanik                 dgoon               jnery          myarif            smofakham
+aaprasad              dgruzdev            jnicasio       myearsley         smui
+aarasappan            dgursoy             jnmauro        myoungblood       smukherjee
+aarefin               dgwood              jnong          mysql             smvaccaro
+aarmas                dhailegeorgi        joawilson      mzamani           snarmeen
+aarroyave             dhamam              jocai          mzepedaaguil      snigam
+aasim                 dhandzlik           jocwilliams    mzhang            snikhil
+aaslov                dhdesouza           jodey          naahassan         snimatullo
+aates                 dhildreth           jodoh          nabchowdhury      snizambad
+aaurora               dhongyi             jodweinstein   nabsyed           snolas
+aavadhani             dhperumal           joeleung       nacchen           snyman
+aavira                dhualong            joeychan       nacharya          soba
+aaydin                diannace            jofranklin     nagnihotri        sochakrabort
+aaysheth              disandovalch        johbernard     nagutierrez       sohshin
+ababbar               diwliu              johnliu        nalewis           sohtsuka
+abadhe                djagnarain          joifan         nanqwang          solhapark
+abahadori             djgold              jomyoung       napopova          somishra
+abaidya               djlambert           jonamartins    naqiu             somunoz
+aball                 djoh                jonicholson    nasweet           sooapark
+abardizbania          djulian             jonsu          natsai            sopjang
+abbhaskar             djyu                jonyin         nazzhou           sortizbetanc
+abeahmad              dkadams             joolee         nbalasubrama      sosarangi
+abenslama             dkharzeev           joosuh         nbasok            sosuresh
+abialkowska           dkirby              joroiland      nbayas            sowu
+abjoshi               dkozakov            joshmathew     nbodduluri        sozturk
+abkanevsky            dkunjadiya          joshumartin    nbosviel          spaci
+abogetti              dlanger             jovvazquezri   nbowers           spandrekar
+aborad                dlhe                joying         nciotoli          spang
+aborcatasciu          dlucksted           jozhao         ncmeloottu        spapazahario
+aborger               dmahalli            jpantano       ncpathak          spapazis
+aborowicz             dmahzabin           jparise        ndcertain         sparvathredd
+abozin                dmale               jparkinson     ndev              spathrose
+abphilip              dmarkov             jpascal        ndheilly          spilkey
+abrady                dmarr               jpcastillo     ndigrandi         spiret
+absalem               dmckinnon           jperezrios     ndnguyen          splee
+abtambe               dmirfenderes        jpeshansky     ndokania          spochron
+aburford              dmorenosanti        jpitt          ndurand           spothumahant
+acage                 dmukherjee          jpmoryl        ndzikowski        spriyadarsha
+acalder               dmulbagalven        jporavanthat   nesteves          spugach
+acali                 dnanjappa           jpwhite        nexposescan       sqavi
+acamino               dnimatullo          jqxiao         neyang            srahmani
+acastiblanco          dnterry             jranjan        nezheng           sraisinghani
+accapua               dobyrne             jrawski        nfaiza            sramanarajan
+acchakravart          dochoi              jrcheung       nfpugliese        sramanarajan.OLD
+acherath              dofu                jrcorbett      nganu             sramjan
+achouhan              dohhlee             jrest          nghoang           sramstrom
+acmarra               dokkang             jrgorman       ngitman           srashidian
+adamare               dongsong            jrimel         ngluck            sretineni
+adanial               dongwhan            jrkamler       ngujarati         srgupte
+adanoji               donshi              jrleeman       nhamdan           srnalluri
+adharan               dotan               jrojahn        nhirtle           srpayne
+adiloreto             doyjang             jrutledge      nichaturvedi      srshende
+ading                 dozhong             jrwei          nidimeglio        ssabaghian
+admannino             dpadhorny           jsaldivar      nigreen           ssagynbayeva
+adpeng                dpare               jsalley        nileong           ssandal
+adpollack             dparedesmeri        jsaltz         niranmanesh       ssarnot
+adrana                dparwana            jsaputo        nisankar          ssarwar
+adrflorio             dpati               jsaxena        nisong            sseepersaud
+adrogers              dpatil              jscanderson    nisoni            ssemerkant
+adubey                dpenchoff           jschuchart     nivsingh          sserbin
+adutt                 dpfennell           jschwedes      njschwartzap      sshaharia
+aecuomo               dpotemkin           jseeliger      nkahmed           sshapourmian
+aeichert              drendina            jseol          nkandru           ssheikhi
+aeltareb              drhamilton          jsgordon       nkatla            sshoque
+aeweiss               dschneble           jsinanan       nkdean            sshrestha
+afahmed               dseddoh             jsistla        nkeer             sshrivastava
+afarhadzadeh          dsforza             jskowalski     nkhalsa           ssivalenka
+afgregory             dshangase           jslogan        nkhandagale       ssjohn
+afrigo                dsingla             jsmaers        nkhatri           sskiena
+afurey                dsli                jsmucker       nkinalis          ssomani
+agaffoor              dslo                jsteier        nkinlock          ssperrottet
+agaikwad              dsmolarski          jsuchan        nkyose            sstoller
+agarforth             dstepanenko         jtalaveragre   nleak             sstoyanov
+agargueta             dstrenski           jtekverk       nlogozzo          ssundar
+agauer                dswesty             jtepan         nlrogers          ssunia
+aghai                 dthanassi           jtevans        nmahamud          ssyedfahad
+agilgomez             dtpham              jtgabrielli    nmaher            ssyritsyn
+agmaharaj             dtsybychev          jtjones        nmanzella         staralekar
+agnsinha              dtung               jtmessina      nmarcella         stawong
+agopalkrishn          duwwang             jtrelewicz     nmathew           stelehany
+agraikos              dvahabli            jtrue          nmehanna          sthaker
+agugel                dvyas               juaalcantara   nmeister          sthorgusen
+agulhane              dwhitty             juffeng        nmenasche         stjjiang
+ahalwah               dwiczer             julima         nmendiratta       stmandell
+ahc                   dwillcox            juliwu         nmeruva           stmccabe
+ahmkhan               dzavala             jumma          nmichielsen       stomar
+ahomayounnik          dziadlou            junding        nmitra            stpak
+ahsingh               eadas               jungshwang     nnadkarni         strainer
+ahurtado              earavera            junholee       nnaitlho          ststern
+ahxiao                eatkinson           junhuzhang     nnakka            stuznik
+aicheng               ebagherizade        junhyelee      nnawal            stzeng
+aidnani               ebartlett           junjiang       nnehaindrani      stzou
+ailyu                 eboria              junkang        nnghiemvu         sudkhan
+airussell             ebreen              junszhou       nniemiec          sukkumar
+ajacovelli            ebremer             juntyao        noibrahim         sunarasimhas
+ajalwan               ebrini              junwang5       nolconner         sunarasimhas.OLD
+ajamieson             ebryski             junxialiu      novsingh          sunghucho
+ajasniew              ecarcelespov        junywang       npahlavan         sunkim2
+ajchan                ecgross             jusandoval     npanagodawet      surmy
+ajchavez              echurch             juschan        nparghi           sushahid
+ajhong                eclemmon            jusliu         npasari           suwei
+ajkoller              ecline              jusong         npayen            svadnerkar
+ajlli                 ecoutsias           justili        npomata           svaldez
+ajmasella             ecowley             jusu           npregosin         svanderpoel
+ajoung                edeturk             juychen        nrajput           svayasi
+ajscarlatos           edma                juyyan         nramdin           svee
+ajtran                edowney             juzou          nreaton           swaxman
+ajwelsh               edzhang             jvansnellenb   nsalekfarama      swchaudhury
+ajyadav               eeryildiz           jvaska         nsampson          swen
+akalugade             efinson             jverbaarscho   nsehgal           sweverma
+akanodia              egebb               jvishal        nshouman          swpaul
+akapote               egentles            jvpepe         nsimakov          sxchen
+akarkare              egouvis             jvu            nsipperly         syaddanapudi
+akarzai               eheywood            jwahhab        nsmehta           syalla
+akaufman              ehspector           jwcross        nsoder            syarma
+akhibovska            ejcarey             jwcusick       nsokolow          syatigala
+akhosronejad          ejguan              jwisdom        nsomani           syatskar
+akhoukhi              ejli                jwlodek        nstreb            sydiaz
+akingan               ejohnfelt           jxue           ntadler           syousef
+akirillov             ekandov             jyerrick       ntardugno         sytlee
+akkale                ekbetancourt        jyluo          ntetrault         tabhatia
+akonosky              ekeck               jzoodsma       ntippabhatla      tadoyle
+akravchuk             ekeough             kabichandani   ntripti           taeklee
+akrowe                ekhew               kadeng         nvafaeinajaf      taeyounkim
+aktyagi               eklau               kadiallo       nvitek            tagiles
+akucich               ekoo                kadill         nvohra            tahkhan
+akuduregundi          elari               kadreher       nvsutherland      tajjung
+akundhuru             elettieri           kafarber       nwein             takther
+akverma               elgchan             kaifzheng      nwweber           talama
+akwakye               elharris            kaili          nxlee             talare
+alabella              eli                 kailiu2        nyfletcher        talin
+alaing                ellai               kailjiang      obellinson        tallison
+alanhuang             elleisenberg        kaimxu         odeshpande        tamislam
+alchung               elmlowe             kaitong        odiamond          tanis
+aldong                elogeswar           kaixichen      odickerson        taryu
+aldraper              elslattery          kamhassan      oeskiocak         tbabu
+alehsu                emacosta            kamrivera      ohaputhanthr      tbertino
+alem                  emarants            kanagarwal     ohyejin           tbrackins
+alexhernande          emarkowitz          kanzhao        okim              tbrinckmann
+alfwu                 emarzigliano        kapatel        okoren            tbrinkley
+algrullon             embriggs            kaporter       omcgranaghan      tburfeind
+alhhuang              emrlin              kapu           omorozova         tbushra
+alianwar              emroberts           karamachandr   omoy              tcanli
+alicwang              emyhand             kargill        onatu             tchatterton
+alietzau              enebet              kasong         oogunfolakan      tchristy
+alifeng               eoruro              katalwar       ooreilly          tchugh
+aliguori              eozkirimli          katschmidt     orambow           tcotroneo
+alindquist            epapadopoulo        kbaylous       osdeshpande       tdawar
+allekim               erandhawa           kbdiaz         oshakkour         tdiprima
+allelin               eraut               kbeckerredd    oshetty           tdviri
+allwong               erbraun             kbelfon        osteele           tema
+almabraham            erfan               kberard        oyang             testro
+almishra              erglukhov           kberghaus      oyasar            tgavryshko
+alokre                ericlin1            kccoughlin     padari            tglotch
+alowell               erizhou             kchetan        paggarwal         tgrgas
+alperezmendo          erkumar             kchitale       pahan             tgrossberndt
+alqin                 erluo               kdas           pallen            tguttula
+alsli                 erosenberg          kdavidson      pamishra          thamada
+alvhsu                errjones            kdehmelt       parjain           thausch
+alynegron             erschroeder         kdemir         parmitage         thdavidson
+amacinnis             erwhuang            kdevedzhiev    patflanagan       therault
+amaffei               esahin              kdhar          patmuller         therodrigues
+amanagarwal           esalman             kdhuri         pavkirkar         thollis
+amanpsingh            esaraivanov         kdyro          pavnkaur          thomlin
+amanzoor              eschiltzrous        kebui          pawu              thren
+amaresca              eshaji              keckartt       payao             thzhou
+amarya                eshetreatkle        kelam          pb                tianyuawang
+amassari              eshih               keliao         pbaliga           tili
+amasuno               eshuryak            kellywang      pcascantebon      timji
+ambbrown              esicoli             kelvlin        pcastillo         timshi
+amccumber             esiegmann           kenchin        pchinthamred      tinggao
+amcelroy              esogut              kenhu          pdalaya           tinghwu
+amchale               esonmez             kennwu         pdamore           tingliu2
+amcpherran            essingh             kereid         pdevarajan        tingslin
+amehla                eswong              kerwood        pdjuric           tinliu
+amehmood              etakeuchi           kevazquez      pdonat            tiwwong
+amgondal              etalis              kevcai         pdongle           tixi
+amibrahim             etchan              kevcheng       pdutta            tiyuan
+amigues               etcheung            keviliu        pechang           tjarrett
+amisaha               ethresher           kevwei         peihsieh          tjohannessen
+amkgupta              etmonaco            kexi           peinwang          tkarwal
+amnoonan              etrommer            kfatema        penzhang          tknoll
+amohamed              etsang              kfernando      pesun             tkohlmann
+amohammadrez          etwest              kflora         pferrero          tkral
+amohanty              etyen               kfryer         pgaikar           tkurc
+amohideen             evalin              kgarg          pganapathi        tla
+amoonilal             evaxie              kgayadhankar   pganesh           tlata
+amrabet               evergaracobo        kgcassar       pgodoy            tloden
+amramroop             evxie               kgjonas        pgoldbart         tlonsway
+amrangwala            ewpeterson          kgoranta       pgoriparthi       tmcgee
+amritpsingh           exiu                kgulati        pgubbala          tmia
+amullhaupt            eylei               khajny         pguo              tmohandas
+amychen5              eyzhu               khasegawa      pgurung           tmoriya
+amyla                 fabdinov            khoh           phariprasad       tmsmyth
+anadelgado            faliang             khumphries     phowlader         tmuntean
+analekseenko          falmodaresit        khyunjae       phtnguyen         tnle
+anarora               faluo               kihan          phyeh             tnsingletary
+ancollins             fang1               kim128         pinlee            toneal
+andcheung             fanliu2             kim169         pinliu            toye
+andguo                fannli              kim65          pjgriffin         tpalit
+andgutierrez          fanwang1            kingle         pkaelbling        tqduong
+andrchu               faoki               kipoon         pkayedpour        tqle
+andrwu                faslanbeigi         kisrani        pkidambi          traj
+andylin2              fatrahman           kissung        pkottapalli       trichen
+anearora              fatsai              kjamal         pkrstic           trli
+anegi                 faye                kjayanettiar   pkuan             trosenlicht
+aneiman               fayyang             kjroberts      pkwoczak          tsclement
+anejoshi              fbasharat           kjtorres       pliu              tshrestha
+anejoshi.OLD          fbischoff           kjun           plorenagodoy      tsinghal
+anemajerova           fcherat             kkamate        pmao              tslewis
+anfrenkel             fcornejofern        kkannapur      pmarla            tsmiley
+angderosa             fcoskun             kkasarapu      pmatera           tteng
+aniksingh             feliang             kkasavajhala   pmcdowall         tthakir
+anisrinivasa          fenzhang            kkaushik       pmdunge           tthulasidas
+anjmoore              fewang              kkayang        pmeade            ttnnguyen
+ankmaheshwar          feyeh               kkirane        pmeda             ttom
+ankrishnan            fgao                kkostyszyn     pmmehta           tweinacht
+anltran               fhchaudhry          kkui           pmscully          tweiwei
+annicoll              fiburke             kkurti         pmuzac            twymore
+anpnguyen             fiowong             kkyeong        pnalluri          txiang
+anpurwar              fjalia              klanzetta      pnookala          tye
+ansabharwal           fjangchup           klhudson       podonnell         tyeh
+ansgandhi             fkarankumar         kljjohnson     ppolak            tyokoyama
+anshen                fkhondker           kllivichuzca   ppriyadarshi      tzwei
+anslade               fladeind            kmadanahitib   praagarwal        uarora
+anthochen             fluo                kmardysilofa   pragupta          uarora.OLD
+antmunoz              fmaisha             kmasarik       praroy            ugarg
+antzhu                fmlopez             kmbala         pratagarwal       ukadakia
+anurizada             fmnoor              kmchang        pratkumar         umoll
+anvinod               fnieto              kmchau         priyjain          umukherjee
+anzaman               forabona            kmcneil        prkkumar          upoddar
+anzhu                 fpocaamoros         kmfallon       prmukhopadhy      urasheed
+anzzhou               frdominguezg        kmhayes        prouth            urehman
+aokisamen             frhu                kmsimon        prreddy           urosani
+apaddayurush          frobayobohor        kmueller       psahu             ushafiq
+apaddayurush.OLD      fsotiropoulo        kmungsoo       psamang           ushassan
+apagarwal             fuliang             kmurgas        psangtani         usunar
+apalit                fwelcome            kpallmann      psekar            utegshbayar
+apalo                 fzali               kpinzon        pshanbhogue       utumuluri
+apalve                gacolella           kpipitone      pskota            uuckun
+apamfilie             gahuja              kprose         psmeyer           uyevarouskay
+aperezantona          gakapoor            kralbano       psokol            vachandramou
+apettenati            gakhan              kramcharan     psonawane         vadabala
+aphope                galing              krayfield      psoundarapan      vanlin
+apilco                garrchen            krdonaldson    pssingh           vanugu
+apizzulli             gashna              krisharma      psurana           vassingh
+aplu                  gatran              krjain         psutter           vbabu
+apolanco              gaumoithe           krkehrli       ptitle            vbayevskiy
+apopoviciu            gazzhang            krmartin       ptonra            vbrill
+aporripiredd          gbalabhadra         krokosz        ptubiolo          vcacciola
+aprabhakar            gbalazsi            krtan          puzheng           vcarter
+apradeep              gbangera            ksabo          pvaishnavi        vchanana
+aprencis              gbermejo            ksampathkuma   pvaska            vduncan
+apsinghal             gbhattachary        kscardigno     pvemula           verana
+apytel                gbiselli            kschweitzer    pvespe            vgoel
+araghani              gbock               kshima         pximello          vhattibettam
+arahimyar             gbosilca            kshou          pyao              vhegde
+arahmati              gbrill              ksirapu        pzbarrett         vhnguyen
+aranasinghe           gchurchill          ksoumahoro     qiangwang         vhuynh
+aravula               gcma                kspuhler       qianywu           vicdai
+arbalasubram          gdhama              ksucich        qiaocwu           vidong
+arcurtis              gdjones             kswayze        qicao             viguo
+ardasgupta            gduarteramos        ktallman       qiding            vikamat
+ardowling             geliang             kthilanka      qihlin            villi
+areisel               gfiakos             ktsteven       qinie             vima
+aresnick              ggandem             ktuzinowski    qinjiang          vincewu
+arfali                ggeorgi             kuagarwal      qinren            vinmirandabr
+argiannakopo          ggopalkrishn        kuchan         qinzhao           vinzheng
+arglenn               gguleria            kumar1         qipan1            visheskumar
+arhossain             ghe                 kumar1.OLD     qirli             vissharma
+arjain                ghothi              kunli          qirwu             vivlam
+arjkrishna            gibrown             kuraj          qxiong            viyee
+armishra              gigill              kuzhong        raagarwal         vjana
+arobert               gimbriano           kveeramah      rabasu            vjishah
+arodriguezd           gipark              kvshah         rachatterjee      vkale
+arojain               girizzo             kwahlin        rachatterjee.OLD  vkhanikaeva
+arpahlavan            gito                kwwalton       rachowdhury       vkodumurumee
+arpbanerjee           gjfuentes           kwyu           raclam            vkondipati
+arpereira             gjiang              kwyyoo         radsrinivasa      vkootagaram
+arsaxena              gjkim               kyadav         raggarg           vlloyd
+arskhan               gkementzidis        kychao         ragte             vloganathan
+arumar                gkowzan             kyethiraj      rahhuang          vlokwani
+aryshrivasta          glarangeira         kylanglois     rahraja           vmaurya
+asadana               gmichaels           kymjames       raich             vmontanez
+asaji                 gmihalache          kyumin         raiislam          vpakala
+asakhan               gmiles              kzzhang        rairahman         vpamula
+asamala               gmogol              lahess         rajatkumar        vperkowski
+asamanta              gmoutsanidis        lawlin         rajdas            vranjan
+asamavedam            gmuradas            lbai           ramhuang          vratnala
+asatam                gnarh               lbozarth       ramorosso         vrustagi
+aschneble             gnwood              lcaradonna     rannadi           vseecharan
+aschorer              goconrosario        lchi           rapeaning         vsnu
+ashaalan              gparkar             lchrastecka    rashanbhag        vstaub
+asharfuddin           gperezgonzal        lcolleyndeso   rashizawa         vtangirala
+asheneman             gprachi             lcooke         ratwi             vvadia
+asillato              grahme              ldavalosalva   raychen2          vvedanair
+asingal               grapacciuolo        ldgraham       rbaheti           vvsharma
+askamat               grkulkarni          lecheung       rbasharat         wadawydiak
+askong                grperlman           ledong         rbertolini        waluo
+asmit                 gsantucci           ledwan         rbhal             wang110
+asofianopoul          gsbeglia            lee104         rbhansali         wang113
+asotocambres          gshivakumar         lee111         rbhowmik          wang132
+asoubki               gshu                lee75          rbiondo           wang148
+asparikh              gstokes             lehhou         rbird             wang154
+asrivastava           gsuczewski          leichen3       rbirnbaum         wang159
+asugumar              gtaylor             leili1         rbodenstein       wang54
+aszekely              guayang             leipan         rboseroy          wang84
+atannenbaum           guayu               leizhou        rbronstein        wangzhang
+ataouil               guazeng             leprentis      rburgert          wawen
+ateklu                guffeng             leriksson      rcconley          wayou
+ateplukhin            gurpreetsing        lernunez       rchabot           wazzhang
+athatikunta           guwechue            lessig         rckline           wbrett
+athennarasu           gvaillant           lesyan         rcrizzo           wcun
+athonis               gverma              letucker       rcsingh           wcunningham
+atosolini             gvorobyev           lgruenburg     rdavuluri         wdaniels
+atpradhan             gyoun               lhinners       rdefrancisco      wecui
+atripoli              gyzhang             lhthorne       rdhaipule         weibhuang
+atsegaimoore          gzakharov           li1            rdhawan           weicdeng
+atsenthilnat          gzborovsky          li20           rdhillon          weichang
+atvarghese            haawilliams         li3            rdogra            weichang.OLD
+aubutt                haenalee            li32           rdrocha           weicheng
+audupashanka          hagguo              liangzhu       rdrucker          weihong
+auhhuang              hahkhan             liannchen      rediaz            weihsu
+avaradarajan          haichwang           lichen8        refem             weihwang
+avisingh              hailxu              lichiang       relkin            weili3
+avonalbertin          hakcakaya           lifwang        relyu             weipeng
+avonderlinde          hallu               lihahuang      renunez           weishen
+avpatil               hamorales           lihazhang      rfkelly           weishi2
+avperry               hanhan              lihexu         rflood            weiszhong
+awalling              hanschoi            lihnguyen      rflorek           weitan
+awardah               hanxwu              lin56          rfrisina          weituchen
+awgriffith            hanzhou1            linchen3       rgadi             weizhu
+awills                haochuwang          lincyu         rgaonkar          welliao
+awjohnso              haolin1             lingjpan       rgautam           wenblu
+aydas                 haolyu              lingyang       rgiles            wenbwang
+ayedageresud          haorazhang          linjjiang      rgmillard         wendazhang
+ayedlarajaia          haotxu              linxu          rgonzalez         wendhu
+ayendluri             haowezheng          linyi          rgzhang           wendu
+ayepuri               haoyzheng           lirzheng       rhande            wendyang
+ayreddy               haraja              liszheng       rharrison         wenhgao
+aysaleem              harbhatt            liu36          rhelbock          wenjihuang
+ayshim                harlee              liu61          rherman           wensliu
+ayusrivastav          hasaadi             liuwang        rhesler           wentawu
+aziafat               hasmoon             liuyang2       rhoffren          wequ
+azuzow                hayyan              liuyzhou       rhua              whiwong
+babrahall             hazhan              liwyang        richatterjee      wholt
+bagarcia              hbchao              ljescobar      richkim           wihu
+ballam                hbien               lkarpuskasan   richlin           withomas
+baminazad             hborchert           lkassetti      rijayaraman       wiwang
+bangchen              hchawla             lko            rikaur            wixiang
+bastark               hchenwu             lkrug          rikeh             wjchen
+bavinash              hdle                llevack        riraquib          wknop
+bbelisle              hdonga              llingda        risjain           wlancer
+bboysan               hduong              lmadiraju      rispatil          wlian
+bbrendan              hechu               lmaeba         ritagarwal        wmichael
+bbulag                heekwon             lmanathungam   riwu              woaks
+bchauhan              henrwang            lmconnolly     rizhuang          wriggs
+bciranni              hetariq             lmdeoliveira   rjayaramared      wsander
+bclevine              hewwang             lmunad         rjbrowne          wsanderson
+bcolle                hhyao               lnazarov       rjdesmond         wshih
+bcuadrado             hipham              lnie           rjeyachandra      wsuttle
+bdanna                hjlynch             lnolasco       rjhuang           wthornton
+bdarapu               hjtrivedi           lonhan         rjleung           wweaver
+bdebarrosfer          hjudson             lorlowski      rjsoni            wweiqiao
+bdelamonica           hkaddour            loswanson      rjwillett         xbarron
+bding                 hkamran             lpanwang       rkhanal           xdmod
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+bejean                hkirby              lpbui          rkhot             xiamu
+bennliu               hle                 lpei           rkidambi          xianaliu
+benyu                 hleung              lpintodealme   rkoots            xiangyuhuang
+bessuman              hmainguy            lprowant       rkyatham          xiangyyang
+bewwong               hmdonaldson         lraguette      rlarsen           xiaocao
+bewwu                 hmoonam             lrastelli      rlpersaud         xiaodliu
+bezzheng              hmoura              lrole          rlsiford          xiaogli
+bfei                  hnegi               lsaleh         rmakheja          xiaohawang
+bfeole                hniederhause        lscampbell     rmalga            xiaohuliu
+bfochtman             hnnguyen            lschappell     rmandloi          xiaokzhao
+bfogg                 hoannguyen          lschutz        rmangalampal      xiaoleyang
+bfutcher              hogao               lshekhar       rmanku            xiaolhu
+bglevine              hokwak              lstrey         rmatsibekker      xiaolhuang
+bgoncalves            holiver             ltalbot        rmax              xiaolucheng
+bgourbal              honghuang           ltngo          rmenezes          xiaotiawang
+bgoyal                honglliu            ltorpey        rmoffitt          xiaotoli
+bguruvayoorm          honglu              ltorrehealy    rmohan            xiaoxyang
+bharrell              hongrzhu            luge           rmudhuganti       xiaoysun
+bhkumar               hongwchen           lujjia         rmuthu            xiaoyuli
+bhowlader             hongyuli            luoshi         rnarvekar         xiaoyuyang
+bhshin                honhuang            lusu           rnorthrup         xicao
+bhsiao                hotnguyen           luzou          rochandramoh      xichen10
+bighimire             hppatil             lvasanthakum   rodtan            xinachen
+bihyu                 hqaiser             lverma         roessig           xingma
+binnchen              hranjan             lvotapka       rohshukla         xingtzhou
+binzhou               hridout             lwollmuth      romjohnson        xingyichen
+bishi                 hrmohammed          lwreid         ronassar          xingywang
+bisshrestha           hrrajput            lyohe          ronwang           xingzguo
+bji                   hsarkar             lyrodrigues    root              xinhahuang
+bjkramer              hschang             maaibrahim     rorosenberg       xinlu2
+bjlai                 hsekino             maalynch       roshukla          xinqian
+bjlee                 hseyyedzadeh        maamandola     roychen1          xintang
+bjnelson              hshafiq             mabruzzeseot   rparsons          xinwang2
+bjqi                  hsiachang           madambrosio    rpatanwadia       xinwang5
+bjugan                hsingathala         madkar         rpatro            xinxu4
+bkhanikaev            hsirotkin           madowling      rpatwary          xinyazheng
+bkovarovic            hsnyders            maedelmann     rperna            xinyin
+blanunez              htalavera           maescobarrod   rpghosh           xiulzhang
+blukacsy              huang54             maggchen       rpmchugh          xiwhuang
+bluy                  huaxiao             maggonzalezg   rpohankar         xixxiong
+bmahal                huichen5            maghazahedi    rpopper           xizhang1
+bmariano              huideng             magmarkowska   rraghunathan      xji
+bmchapman             huidliu             maguevarra     rrani             xjiao
+bmhenn                huisong             mahahn         rristowhadli      xqliu
+bmhyland              huixu1              mahhasan       rritu             xsha
+bmkaufman             huixzhu             mahiralam      rsamulyak         xshuqian
+boakley               hullee              maiyedun       rsandhu           xuaqi
+bocao                 hungwchen           makhdhor       rsarker           xuaxu
+bohhuang              huntwale            makinboade     rsejour           xudeng
+boisuh                huyzhang            makmalone      rsher             xuebwang
+borwang               hvannieuwenh        makowalchyk    rshilkrot         xueqli
+bossun                hvig                maksen         rshimogawa        xuxie
+bowusufrimpo          hvijayakumar        maliyari       rsihag            xyuan
+bozhao1               hwoh                malvin         rsison            yaagarwal
+bpamuk                hxing               mamahzabin     rsmolinski        yakang
+bpilosov              hyejichoi           mamandola      rsoori            yang28
+bquang                hyemkim             mamlan         rspowers          yang34
+bquang.OLD            hyeocho             maochoa        rstusalitus       yangfwu
+brampanellid          hyeonkyung          mapak          rtamarkin         yangli10
+brbartlett            hykoo               mapang         rtelikicherl      yangli9
+brgraham              hymin               marif          rthacker          yanglu2
+brlai                 hyochung            marioreyes     rtrybulski        yangxie
+brlgonzalez           hyuchung            markhangelsk   ruhipatel         yangzhang
+brma                  hyulim              markong        ruicxu            yangzhou
+brmcgovern            hyunjuncho          masharma       ruiding           yanwang2
+brmoses               hyunsikim           masong         ruihechen         yaoli2
+brpark                hzhan               matique        ruiqiwang         yaozou
+brsantos              hzohair             matjones       ruishi            yashu
+brshao                iabbasparker        mattchang      rulliu            yaspatel
+brwwang               iakgun              mavanalstine   runcli            yaxuan
+bryang                iakim               mawwa          ruossun           yazadeh
+brzhou                ialabed             maxmuller      ruparekh          yazou
+brzhu                 ibilkhu             mazhao         rusharma          ybajaj
+bsbernstein           ibipul              mazzimontire   ruyu              ychao
+bschiller             ibolger             mbandham       rwales            yding
+bsen                  ibromberg           mbarbosa       rwilson           yehu
+bshan                 icisternino         mbastan        rxli              yejikim3
+bsheller              ifaridi             mbender        ryachen           yeke
+bsheridan             igkane              mbianchi       ryanglee          yellaham
+bspitzbart            igrehn              mbliss         ryao              yenwchen
+bsterling             ihubbard            mboisvert      rycchan           yenwechen
+bsundahl              iinani              mbolko         rychin            yeonskang
+btenreiro             ijacob              mborczuk       ryengel           yhannun
+btmichalowic          ijhuang             mbowen         rygeorge          yhasib
+buli                  ikao                mbozok         rysalernoeic      yhochberg
+bvilla                ikotler             mbrunger       rzlin             yibqi
+byungjkim             iloop               mbuskirk       saachowdhury      yichuang
+caaugustine           ilopezcoto          mcaponegro     saaikhan          yiclin
+caaventura            imarchitelli        mcfoley        sabedin           yicozhu
+calyu                 inikiforakis        mchio          sabergman         yidcheng
+camcdonough           iojima              mcirrito       sabeykoon         yifagao
+caponteriver          iosipitan           mckoch         sabousamra        yifasun
+caprea                iouthwaite          mclim          saconstantin      yifewu
+cargomes              iparaskevako        mcng           sadas             yigao2
+carhall               ipjohnson           mconners       sadeshpande       yihanwang
+carlliu               ipunn               mdabhole       sadsharma         yihsu
+carlopez              iramakrishna        mdarita        saerkim           yihua
+carty                 ishin               mdatar         saffan            yijiang3
+cballena              isiergiej           mdavariesfah   sagchandrash      yijing
+cbehan                istaylor            mdeisler       saichowdhury      yijliu
+cbetz                 itaradachuk         mdelasaysork   saihaque          yijtian
+cblackwell            itrivedi            mdhuang        saismail          yijzhu
+cboon                 iurbinahenri        mdovedytis     sakader           yiliu4
+cbrandon              ivalin              mdsweeney      sakhalifa         yilma
+cbudd                 ivanlin             mdwalam        sakinney          yimzhao
+cbunner               ivaratharaja        meemcnamara    sakotagiri        yimzhu
+ccardetti             iwankavala          meijli         samachen          yingczhou
+ccarew                jaapatel            meisanchezpe   samesingh         yingfan
+ccdressler            jabauer             meisong        samhoque          yinglu1
+ccgordon              jabryan             meliasi        samichowdhur      yinou
+cchecastaldo          jacacosta           meliot         samrosner         yinxzhang
+ccioffi               jaccao              memendi        samung            yinyou
+ccolosqui             jackili             mempark        samvasquez        yipli
+ccorbo                jacobsmith          menalam        sangyoon          yiqguo
+ccpeterson            jacojoseph          menchowdhury   sarani            yittian
+cdehury               jacparker           mengao         sasaluja          yiwasaki
+cdehury.OLD           jacsegal            mengjliu       sashrestha        yiwchao
+cdelorenzo            jaejeong            menglin1       sasnyder          yixcui
+cdreyer               jaevangelist        mengrzhang     sastephens        yiyayu
+cegarrison            jaeyojung           mengtliu       sasurana          yiyizhou
+celkhoury             jafinn              mengwu         saswang           yizholi
+cexu                  jafu                mengxwang      satsaha           yjetwani
+ceyeung               jagluzman           mesch          saukumar          ykakade
+cfeldman              jaharora            meserranosos   saupaul           ykhaliqui
+cflagg                jahua               meyasmin       saursingh         ykuyu
+cfnapoli              jaimehta            meyue          savargas          ymaung
+cfontanini            jakaczmarzyk        mezaman        saysharma         ymondal
+cforan                jakhil              mfbugallo      sazchowdhury      yneelam
+cgarybicas            jakkatz             mferdman       sbadlia           yohe
+cgauthier             jalbanes            mfierek        sbaines           yokato
+cgobler               jalbertigles        mfirmansyah    sbajjuri          yokee
+cgrieco               jalzamoramar        mfite          sbanam            yoki
+cgueli                jamarini            mforslund      sbatheja          yomma
+cguerraamori          jamoscosonun        mfoydl         sbeesabathun      yongjzhang
+chacho                jange               mfucci         sbeg              yongmchoi
+chahan                jannguyen           mgarciadiaz    sbenz             yongshin
+chalpern              janswong            mgcortes       sbhuma            yonxiang
+changhpark            jaschow             mghaderibane   sbillah           yoshen
+changjli              jashukla            mghogale       sbinnamangal      youcha
+chanzhang             jasjiang            mgholamianji   sbire             youngkwon
+charwong              jasolau             mgivehki       sbirrer           younkang
+chccai                jasonwang           mgwhite        sboddeti          yousshin
+chdang                jaswsingh           mhanubal       sboppudi          ypichkar
+chen110               jathoffman          mhare          sbrahmadevar      yrhamatzada
+chen147               jaygutierrez        mhaziz         sbscott           ysingh
+chen15                jazpurua            mhijikata      sburgert          ysoh
+chen157               jbak                mhorowitz      scberg            yson
+chen175               jbakalis            mhott          scduppala         ysoroka
+chen181               jbalsamo            miachristie    scentorrino       ytham
+chen182               jbarrantes          miahe          schheda           yuanjchen
+chen32                jbarron             mianchen       schiappone        yuanzhao
+chen77                jbernauer           mibbowman      schook            yuasong
+chencjiang            jbeutel             michaliang     scokro            yuchen4
+chenclu               jbhambure           michelhuang    scsteiger         yuchen7
+chenczhu              jbickel             michellhuang   sdedhia           yuchzhou
+chenghli              jbkelly             michhuang      sdefaz            yucma
+chengklin             jbohne              micnicolette   sdescalso         yucpu
+chengpsun             jbraick             micxu          sdhalleweyn       yucsun
+chenliang             jbrimlow            miczhao        sdisalvo          yucxing
+chetheringto          jbrunelle           miduan         sdivilov          yucye
+cheye                 jbuckley            mignatov       sdsouza           yudding
+chezheng              jbuckley.OLD        mihur          sdssingh          yudichen
+chgraham              jburzachiell        mijia          sebramirezvi      yuechen4
+chguo                 jcano               mijrivera      seg               yuefandeng
+chhhogan              jcaputi             milobi         seojchang         yuehuang
+chichiang             jcassella           miloska        seongan           yuejin
+chienlee              jcespedes           mimak          seonghjeong       yuewang6
+chihhchang            jchaillet           minghazhang    seongioh          yuewang7
+chihu                 jchivu              mingsun        seshin            yuewlin
+chiuyu                jchlee              mingyli        sestoller         yuezhao2
+chlow                 jcmichel            mingyzhang     seunchoi          yufchen
+chmorales             jcodere             minhwang       sexia             yuhajiang
+chodgdon              jcolaizzo           minkwan        sfardeen          yuhwu
+chou                  jcollier            miray          sfarhat           yulma
+chriskim              jconesa             mireza         sfarnan           yuluwang
+christwong            jdarling            miswong        sfinch            yulyu
+chtian                jdcraig             mjadhav        sfiola            yumichen
+chuahuang             jdeneau             mjavanmard     sfluo             yunhxu
+chugo                 jdesilva            mjbonney       sgajjala          yunjeon
+chuntchan             jdovi               mjchun         sgala             yunlzhang
+chuzhu                jdscully            mkaltak        sgenovese         yunpan
+chuzou                jdubnau             mkamiya        sghavamnia        yupeng
+chyou                 jdwarren            mkanasani      sghavat           yuqianwu
+chyyoon               jecao               mkanasani.OLD  sgholami          yuqiao
+chzuo                 jefzhong            mkapadia       sghorashi         yushuang
+cikang                jegaillard          mkaribian      sgopalan          yusjin
+ciriccio              jejchan             mkhemchandan   sgoswami          yuthe
+cjbyrnes              jelau               mkishore       sgrao             yuttian
+cjzheng               jelsoudy            mkochert       sgrieninger       yuwang7
+ckapre                jemak               mkoga          sgurram           yuwzhang
+ckarwan               jemchen             mkondeti       sguru             yuxia4
+ckelton               jenfu               mkonovalyuk    sgwilliams        yuxlin
+ckochath              jepace              mkoraiem       sgyuho            yuxuanzhang
+cksullivan            jerlin              mkpatel        shaamin           yuxushi
+cleeliang             jeryeung            mkritzer       shakislam         yuxwu
+clegett               jesgoldstein        mksanda        shalirou          yuyguo
+clfischer             jeslong             mkurakula      shanhe            yuzhwang
+clongarini            jessewang           mlaul          shanlin2          yyokoi
+clsears               jettran             mlauterbur     shaoliu           zafahmad
+cltong                jevalle             mlcollier      shaowang          zalseika
+cltucker              jeyeung             mlng           shaqin            zariahmed
+cluhmann              jeyyoo              mlondoo        sharinarayan      zballard
+clwolfe               jfmoon              mloverde       shawmathew        zbhinderwala
+cmack                 jgaige              mmadeira       shcchakrabor      zcheslog
+cmcarey               jgajello            mmahboob       shclay            zcytryn
+cmcgrew               jgergen             mmahim         shdesai           zdoora
+cmehndiratta          jglazar             mmaitra        shdixit           zdowling
+cmflynn               jglimm              mmakeev        shdixit.OLD       zdupont
+cmfoley               jgurevitch          mmarder        shechoi           zexizhang
+cmjurgensen           jhajagos            mmaskaliova    shengzhu          zeyao
+cmkennedy             jharder             mmasoumi       shengzwang        zezhu
+cmoczygemba           jheerwig            mmatero        shenjin           zfallon
+cmoote                jheinz              mmaung         sheshao           zgrandison
+cmorantesari          jheraghty           mmcduffie      shexiong          zgungor
+cmwoo                 jhjung              mmcneill       shikgupta         zhacai
+cnoe                  jhollister          mmerenstein    shilgupta         zhage
+cnoutsos              jhpark              mmilhaven      shilliu           zhagu
+codlam                jiabwang            mmimurphy      shiltian          zhang100
+cohwarner             jiachzhu            mmursheed      shitsai           zhang110
+cojiang               jiacxu              mniznikiewic   shivansharma      zhang118
+cokeoma               jiahuwang           mnovotny       shivgupta         zhang123
+coleary               jiajgao             moamin         shiyuawang        zhang133
+concao                jiaji               mobusan        shkhalid          zhang142
+conliu                jiakwang            moewilliams    shmmohammed       zhang152
+cpercival             jialai              moflus         shmondal          zhang173
+cpethe                jialin1             mogao          shopatel          zhanyang
+cpinizzotto           jiamili             mogoel         shperalta         zhaoliu
+cplizio               jiamwu              mohassan       shrajput          zhchai
+cprasad               jianfeng            mojia          shroy             zhddong
+cqiu                  jianflin            molssi000      shrraman          zhedzhang
+cradke                jianhan             molssi001      shsaha            zhefang
+crcollinswor          jianjliu            molssi002      shshekhar         zheng13
+crfernandesv          jianmtan            molssi003      shshekhar.OLD     zheng30
+csangiovanni          jiannyang           molssi004      shsin             zhengxwang
+csantoni              jianxiozhang        molssi005      shssridhar        zhenjhuang
+csasmith              jiaojiang           molssi006      shtao             zhenliu
+cschwaner             jiapatel            molssi007      shuaguo           zhenlu
+cshiveshwark          jiasu               molssi008      shubwang          zhenqian
+csiebor               jiatian             molssi009      shuhe             zhenwu
+csimmerling           jiawang1            molssi010      shujia            zhenxliu
+csingleton            jiaweichen          molssi011      shyyoo            zheychen
+cstussman             jiawezhu            molssi012      shyyuan           zhezhou1
+csyreilly             jiaxuyu             molssi013      shzzhou           zhibwang
+cthakur               jiayeguo            molssi014      siasun            zhibyang
+ctinker               jiayyan             molssi015      sichchen          zhideng
+ctustin               jibbai              molssi016      sicheliu          zhihhe
+cuwang                jichao              molssi017      sichhabra         zhihhuang
+cvorkas               jiddong             molssi018      sichliu           zhijli
+cweistuch             jiechen3            molssi019      sigadkar          zhimalin
+cwoellhof             jiemchen            molssi020      siggupta          zhipxu
+cxi                   jiemzeng            molssi021      sihqian           zhiwlin
+cyanagisawa           jienzhu             molssi022      sijhuang          zhixzhang
+cyluo                 jieyang             molssi023      sijjiang          zhiye
+cyoungflesh           jihlin              molssi024      sijliu            zhke
+czhen                 jihoopark           molssi025      silai             zhlee
+d9wang                jihuynh             molssi026      singanne          zhonliang
+dabelinsky            jihyepark           molssi027      singh4            zhouyu1
+dagolden              jiikim              molssi028      sinhong           zhuhli
+dagrange              jijin               molssi029      sinlin            zhuxie
+daiwang               jilao               molssi030      sinsmith          zhwong
+dalpancakmak          jiliu1              molssi031      sirle             zhxia
+damcintyre            jimlin              molssi032      sishizawa         zidiao
+damiruddin            jimun               molssi033      siskhakov         ziguan
+damoses               jin                 molssi034      siuchan           zijiao
+dandrew               jinghzhou           molssi035      siwewang          zijizhou
+dangelidis            jingwenli           molssi036      sixliu            zikhan
+danieliang            jingwezhang         molssi037      siyadav           zilinchen
+danitorresra          jingwliu            molssi038      siyao             zilwu
+danizheng             jinkokim            molssi039      siyimaya          zirliu
+dantorres             jinwang2            morahimi       siyzou            zishao
+dantyu                jinwei              moriasaranib   sizahid           ziweiwang
+danwei                jinyhu              mozhao         sizzheng          ziwyu
+daoconnell            jinyinwang          mperess        sjaffary          zixli
+dappark               jinyli              mpersch        sjamshad          ziyli
+darkow                jinyuyang           mpetrusky      sjeevan           ziyozhang
+darlin                jinyxu              mpkatz         sjens             ziyye
+darvind               jinzwang            mpsantomauro   sjiecheng         zkrayem
+darzeng               jiqian              mquispecarba   sjnelson          zlyu
+dathanasakos          jiychong            mradfar        sjyang            zmou
+daultmccoy            jiyim               mrahimibolda   skade             zniu
+davidlin              jiyjung             mrakhar        skagana           zoanderson
+davizhao              jiyounpark          mrashid        skalam            zoxie
+davliang              jiyuliu             mrathore       skalva            zqiao
+davsilverman          jiyuyang            mrayeesuddin   skann             zsongzhu
+dawan                 jjcarter            mrehan         skapse            zuzheng
+dawei                 jjguo               mreuter        skapur            zwray
+dawendt               jjjones             mrichter       skarnik           zye
+dawhu                 jjnielsen           mrius          skatariya         zzaidi
+daxxie                jkable              mrkumar        skavuri           zzhuang
+dayeung               jkiryluk            mrosati        sketchum          zzoya
+dayyan                jkodner             mrsun          skobayashi
+dayyoon               jkohara             msardis        skogilathota
+dbasu                 jkonopka            msavenkov      skomatireddy
+dbluestein            jkottmann           msayana        skoppuravuri
+(base) [ehspector@milan1 home]$ cd ..
+(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/
+(base) [ehspector@milan1 AMS536]$ ls
+EVE_Lig_nH.mol2    1eve_Rec_nH.mol2  2018  2021  2024            junk.txt
+EVE_Lig_wH.mol2    1eve_Rec_wH.mol2  2019  2022  2025            zzz.anchors
+EVE_Rec_nHDMS.dms  2017              2020  2023  get_anchors.py  zzz.programs
+(base) [ehspector@milan1 AMS536]$ cd 2025
+(base) [ehspector@milan1 2025]$ ls
+EVE_DOCK_VS      INSPH           rotations  wed_humpday.txt
+additional_files  robbashrc_file  test4.tar
+(base) [ehspector@milan1 2025]$ vi test4.tar
+(base) [ehspector@milan1 2025]$ pwd
+/gpfs/projects/AMS536/2025
+(base) [ehspector@milan1 2025]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/test4.tar test4.tar
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN  test4.tar
+(base) [ehspector@milan1 Tutorials]$ mv test4.tar 2w26/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin     007_cartesian_min  Notes.txt
+_surface_spheres  005_rigid         008_rescore        test4.tar
+_gridbox          006_flex_docking  commands.txt
+(base) [ehspector@milan1 2w26]$ tar -xf test4.tar
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin     007_cartesian_min  commands.txt
+_surface_spheres  005_rigid         008_rescore        Notes.txt
+_gridbox          006_flex_docking  2W26               test4.tar
+(base) [ehspector@milan1 2w26]$ cd 2W26/
+(base) [ehspector@milan1 2W26]$ ls
+_structure  002_spheres  003_grid  004_dock
+(base) [ehspector@milan1 2W26]$ cd 004_dock/
+(base) [ehspector@milan1 004_dock]$ ls
+fps_footprint_scored.txt      01fps_scored.mol2  02rgd.in           03fad.out
+fps_footprint_scored.txt.pdf  01fps.sh           02rgd.log          03fad_scored.mol2
+fps_hbond_scored.txt          01min.in           02rgd.out          03fad.sh
+fps.in                        01min.log          02rgd_scored.mol2  04flx.in
+fps.log1                      01min.out          02rgd.sh           04flx.sh
+fps.log2                      01min_scored.mol2  03fad.in           old_01min.in
+fps.out                       01min.sh           03fad.log
+(base) [ehspector@milan1 004_dock]$ vi 02rgd.in
+(base) [ehspector@milan1 004_dock]$ cd ../../
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin     007_cartesian_min  commands.txt
+_surface_spheres  005_rigid         008_rescore        Notes.txt
+_gridbox          006_flex_docking  2W26               test4.tar
+(base) [ehspector@milan1 2w26]$ mv 005_rigid/  005_dock/
+(base) [ehspector@milan1 2w26]$ mv 006_flex_docking/ 006_virtual_screening
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin          007_cartesian_min  commands.txt
+_surface_spheres  005_dock               008_rescore        Notes.txt
+_gridbox          006_virtual_screening  2W26               test4.tar
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_2w26
+(base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/02rgd.in 005_dock/
+(base) [ehspector@milan1 2w26]$ cd 005_dock/
+(base) [ehspector@milan1 005_dock]$ ls
+rgd.in    rigid.in   rigid.out_conformers.mol2  rigid.sh
+rigid_2.sh  rigid.out  rigid.out_scored.mol2
+(base) [ehspector@milan1 005_dock]$ rm rigid.in
+(base) [ehspector@milan1 005_dock]$ mv 02rgd.in rigid.in
+(base) [ehspector@milan1 005_dock]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.out_conformers.mol2  rigid.out_scored.mol2  rigid.sh
+(base) [ehspector@milan1 005_dock]$ rm rigid.out_conformers.mol2
+(base) [ehspector@milan1 005_dock]$ rm rigid.out_scored.mol2
+(base) [ehspector@milan1 005_dock]$ vi rigid.in
+(base) [ehspector@milan1 005_dock]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.sh
+(base) [ehspector@milan1 005_dock]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd 001_structure/
+(base) [ehspector@milan1 001_structure]$ la
+-bash: la: command not found
+(base) [ehspector@milan1 001_structure]$ ls
+w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
+w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ../005_dock/
+(base) [ehspector@milan1 005_dock]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid.sh
+(base) [ehspector@milan1 005_dock]$ vi rigid.in
+(base) [ehspector@milan1 005_dock]$ mkdir rigid_docking
+(base) [ehspector@milan1 005_dock]$ mv rigid.in rigid_docking/
+(base) [ehspector@milan1 005_dock]$ mv rigid.sh rigid_docking/
+(base) [ehspector@milan1 005_dock]$ mv rigid_2.sh rigid_docking/
+(base) [ehspector@milan1 005_dock]$ rm rigid.out
+(base) [ehspector@milan1 005_dock]$ ls
+rigid_docking
+(base) [ehspector@milan1 005_dock]$ mkdir flex_docking
+(base) [ehspector@milan1 005_dock]$ mkdir_fixed_anchor_docking
+-bash: mkdir_fixed_anchor_docking: command not found
+(base) [ehspector@milan1 005_dock]$ mkdir fixed_anchor_docking
+(base) [ehspector@milan1 005_dock]$ ls
+fixed_anchor_docking  flex_docking  rigid_docking
+(base) [ehspector@milan1 005_dock]$ cd rigid_docking/
+(base) [ehspector@milan1 rigid_docking]$ ls
+rigid_2.sh  rigid.in  rigid.sh
+(base) [ehspector@milan1 rigid_docking]$ vi rigid.in
+(base) [ehspector@milan1 rigid_docking]$ vi rigid_2.sh
+(base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
+(base) [ehspector@milan1 rigid_docking]$ ls
+rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
+(base) [ehspector@milan1 rigid_docking]$ vi rigid.out
+(base) [ehspector@milan1 rigid_docking]$ vi rigid.in
+(base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
+(base) [ehspector@milan1 rigid_docking]$ ls
+rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
+(base) [ehspector@milan1 rigid_docking]$ vi rigid.out
+(base) [ehspector@milan1 rigid_docking]$ vi rigid.in
+(base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
+(base) [ehspector@milan1 rigid_docking]$ ls
+rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
+(base) [ehspector@milan1 rigid_docking]$ grep -c "Name" rigid_scored.mol2
+(base) [ehspector@milan1 rigid_docking]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin          007_cartesian_min  Notes.txt
+_surface_spheres  005_dock               008_rescore        Robs_2w26
+_gridbox          006_virtual_screening  commands.txt       test4.tar
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/03fad.in 005_dock/fixed_anchor_docking/
+(base) [ehspector@milan1 2w26]$ cd 005_dock/fixed_anchor_docking/
+(base) [ehspector@milan1 fixed_anchor_docking]$ ls
+fad.in
+(base) [ehspector@milan1 fixed_anchor_docking]$ mv 03fad.in fad.in
+(base) [ehspector@milan1 fixed_anchor_docking]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cp rigid_docking/rigid_2.sh fixed_anchor_docking/fad.sh
+(base) [ehspector@milan1 005_dock]$ cd fixed_anchor_docking/
+(base) [ehspector@milan1 fixed_anchor_docking]$ ls
+fad.in  fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.in
+(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ bash fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ ls
+fad.in  fad.out  fad_scored.mol2  fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.out
+(base) [ehspector@milan1 fixed_anchor_docking]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cp fixed_anchor_docking/fad.sh flex_docking/flex.sh
+(base) [ehspector@milan1 005_dock]$ cd ..
+(base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/04flx.in 005_dock/flex_docking/flex.in
+(base) [ehspector@milan1 2w26]$ cd 005_dock/flex_docking/
+(base) [ehspector@milan1 flex_docking]$ ls
+flex.in  flex.sh
+(base) [ehspector@milan1 flex_docking]$ vi flex.in
+(base) [ehspector@milan1 flex_docking]$ vi flex.sh
+(base) [ehspector@milan1 flex_docking]$ bash flex.sh
+(base) [ehspector@milan1 flex_docking]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan1 flex_docking]$ grep -c "Name" flex_scored.mol2
+(base) [ehspector@milan1 flex_docking]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cd flex_docking/
+(base) [ehspector@milan1 flex_docking]$ pwd
+/gpfs/home/ehspector/AMS_536/Tutorials/2w26/005_dock/flex_docking
+(base) [ehspector@milan1 flex_docking]$ cd ../fixed_anchor_docking/
+(base) [ehspector@milan1 fixed_anchor_docking]$ ls
+fad.in  fad.out  fad_scored.mol2  fad.sh
+(base) [ehspector@milan1 fixed_anchor_docking]$ cd ../rigid_docking/
+(base) [ehspector@milan1 rigid_docking]$ ls
+rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
+(base) [ehspector@milan1 rigid_docking]$ cd ../../
+(base) [ehspector@milan1 2w26]$ cd ../
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/
+(base) [ehspector@milan1 5EEN]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan1 5EEN]$ mv 005_virtual_screen/ 005_dock
+(base) [ehspector@milan1 5EEN]$ cd 005_dock/
+(base) [ehspector@milan1 005_dock]$ ls
+(base) [ehspector@milan1 005_dock]$ mkdir rigid fixed_anchor flex
+(base) [ehspector@milan1 005_dock]$ ls
+fixed_anchor  flex  rigid
+(base) [ehspector@milan1 005_dock]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid_2.sh 5EEN/005_dock/rigid/
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/005_dock/rigid/
+(base) [ehspector@milan1 rigid]$ ls
+rigid_2.sh
+(base) [ehspector@milan1 rigid]$ vi rigid_2.sh
+(base) [ehspector@milan1 rigid]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 5EEN]$ cd 005_dock/
+(base) [ehspector@milan2 005_dock]$ ls
+fixed_anchor  flex  rigid
+(base) [ehspector@milan2 005_dock]$ cd rigid/
+(base) [ehspector@milan2 rigid]$ ls
+rigid_2.sh
+(base) [ehspector@milan2 rigid]$ touch rigid.in
+(base) [ehspector@milan2 rigid]$ vi rigid_2.sh
+(base) [ehspector@milan2 rigid]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i rigid.in
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+                                             ligand_atom_file [database.mol2] ():5EEN.lig.min_scored.mol2
+                                            limit_max_ligands [no] (yes no):
+                                                skip_molecule [no] (yes no):
+                                           read_mol_solvation [no] (yes no):
+                                               calculate_rmsd [no] (yes no):yes
+                                       use_rmsd_reference_mol [no] (yes no):yes
+                                      rmsd_reference_filename [ligand_rmsd.mol2] ():5EEN.lig.min_scored.mol2
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):
+                                           automated_matching [yes] (yes no):
+                                           receptor_site_file [receptor.sph] ():../../002_surface_spheres/selected_spheres.sph
+                                             max_orientations [1000] ():
+                                              critical_points [no] (yes no):
+                                            chemical_matching [no] (yes no):
+                                           use_ligand_spheres [no] (yes no):
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):
+                                     grid_score_rep_rad_scale [1] ():
+                                         grid_score_vdw_scale [1] ():
+                                          grid_score_es_scale [1] ():
+                                          grid_lig_efficiency [no] (yes no):
+                                       grid_score_grid_prefix [grid] ():../../003_gridbox/grid
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+                                              minimize_ligand [yes] (yes no):yes
+                                       simplex_max_iterations [1000] ():
+                               simplex_tors_premin_iterations [0] ():
+                                           simplex_max_cycles [1] ():
+                                       simplex_score_converge [0.1] ():
+                                       simplex_cycle_converge [1.0] ():
+                                           simplex_trans_step [1.0] ():
+                                             simplex_rot_step [0.1] ():
+                                            simplex_tors_step [10.0] ():
+                                            simplex_final_min [no] (yes no):
+                                          simplex_random_seed [0] ():
+                                        simplex_restraint_min [no] (yes no):
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+                                                   atom_model [all] (all | united):
+                                                vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+                                               flex_defn_file [flex.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+                                              flex_drive_file [flex_drive.tbl] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+                                        ligand_outfile_prefix [output] ():rigid
+                                          write_mol_solvation [no] (yes no):
+                                           write_orientations [no] (yes no):
+                                        num_scored_conformers [1] ():
+                                              score_threshold [100.0] ():
+                                                 rank_ligands [no] (yes no):
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+Could not open 5EEN.lig.min_scored.mol2 for reading.  Program will terminate.
+(base) [ehspector@milan2 rigid]$ cd ../../004_energymin/
+(base) [ehspector@milan2 004_energymin]$ ls
+een.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan2 004_energymin]$ cd ../005_dock/rigid/
+(base) [ehspector@milan2 rigid]$ ls
+rigid_2.sh  rigid.in
+(base) [ehspector@milan2 rigid]$ vi rigid.in
+(base) [ehspector@milan2 rigid]$ vi rigid.in
+(base) [ehspector@milan2 rigid]$ bash rigid_2.sh
+(base) [ehspector@milan2 rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out
+(base) [ehspector@milan2 rigid]$ vi rigid.out
+(base) [ehspector@milan2 rigid]$ vi rigid.in
+(base) [ehspector@milan2 rigid]$ bash rigid_2.sh
+(base) [ehspector@milan2 rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid_scored.mol2
+(base) [ehspector@milan2 rigid]$ vi rigid.out
+(base) [ehspector@milan2 rigid]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/
+(base) [ehspector@milan2 rigid]$ rm rigid.in
+(base) [ehspector@milan2 rigid]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid.in 5EEN/005_dock/rigid/rigid.in
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/
+(base) [ehspector@milan2 rigid]$ ls
+rigid_2.sh  rigid.in  rigid.out  rigid_scored.mol2
+(base) [ehspector@milan2 rigid]$ vi rigid.in
+(base) [ehspector@milan2 rigid]$ bash rigid_2.sh
+(base) [ehspector@milan2 rigid]$ ls
+rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2
+(base) [ehspector@milan2 rigid]$ grep -c "Name" rigid_scored.mol2
+(base) [ehspector@milan2 rigid]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.in 5EEN/005_dock/fixed_anchor/fad.in
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.sh 5EEN/005_dock/fixed_anchor/fad.sh
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/fixed_anchor/
+(base) [ehspector@milan2 fixed_anchor]$ ls
+fad.in  fad.sh
+(base) [ehspector@milan2 fixed_anchor]$ vi fad.in
+(base) [ehspector@milan2 fixed_anchor]$ vi fad.sh
+(base) [ehspector@milan2 fixed_anchor]$ bash fad.sh
+(base) [ehspector@milan2 fixed_anchor]$ ls
+fad.in  fad.out  fad_scored.mol2  fad.sh
+(base) [ehspector@milan2 fixed_anchor]$ grep -c "Name" fad_scored.mol2
+(base) [ehspector@milan2 fixed_anchor]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.in 5EEN/005_dock/flex/flex.in
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.sh 5EEN/005_dock/flex/flex.sh
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
+(base) [ehspector@milan2 flex]$ ls
+flex.in  flex.sh
+(base) [ehspector@milan2 flex]$ vi flex.in
+(base) [ehspector@milan2 flex]$ bash flex.sh
+exit
+(base) [ehspector@milan2 flex]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2
+(base) [ehspector@milan2 flex]$ vi flex.out
+(base) [ehspector@milan2 flex]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ rm flex.out
+(base) [ehspector@milan2 flex]$ bash flex.sh
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ vi flex.
+(base) [ehspector@milan2 flex]$ vi flex.out
+(base) [ehspector@milan2 flex]$ cd ..
+(base) [ehspector@milan2 005_dock]$ ls
+fixed_anchor  flex  rigid
+(base) [ehspector@milan2 005_dock]$ cd flex/
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 1O86]$ mv 005_virtual_screen/ 005_dock
+(base) [ehspector@milan2 1O86]$ cd 005_dock/
+(base) [ehspector@milan2 005_dock]$ mkdir rigid fixed_anchor flex
+(base) [ehspector@milan2 005_dock]$ cd ../../
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.in 1O86/005_dock/rigid/rigin.in
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.sh 1O86/005_dock/rigid/rigin.sh
+cp: cannot stat '5EEN/005_dock/rigid/rigid.sh': No such file or directory
+(base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid_2.sh 1O86/005_dock/rigid/rigin.sh
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/005_dock/rigid/
+(base) [ehspector@milan2 rigid]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP AMS_548 % cd ../AMS_691
+(base) supremestudier@Evans-MBP AMS_691 % ls
+AMS691_01.pdf	Lectures	Projects	Text_book
+(base) supremestudier@Evans-MBP AMS_691 % mkdir PyTorch
+(base) supremestudier@Evans-MBP AMS_691 % cd ../AMS_536
+(base) supremestudier@Evans-MBP AMS_536 % ls
+Tutorial				project.example.dGhyd.pdf
+project.example.MMPS.pdf		zzz_2025_01_29a_seawulf_notes.docx
+(base) supremestudier@Evans-MBP AMS_536 % cd Tutorial
+(base) supremestudier@Evans-MBP Tutorial % ls
+O86		2w26		5EEN		folders.txt
+(base) supremestudier@Evans-MBP Tutorial % cd 5EEN
+(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ cd 1O86/005_dock/rigid/
+-bash: cd: 1O86/005_dock/rigid/: No such file or directory
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd 1O86/005_dock/rigid/
+-bash: cd: 1O86/005_dock/rigid/: No such file or directory
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/rigid/
+(base) [ehspector@milan1 rigid]$ ls
+rigin.in  rigin.sh
+(base) [ehspector@milan1 rigid]$ mv rigin.in rigid.in
+(base) [ehspector@milan1 rigid]$ mv rigin.sh rigid.sh
+(base) [ehspector@milan1 rigid]$ vi rigid.in
+(base) [ehspector@milan1 rigid]$ cd ../../004_energymin/
+(base) [ehspector@milan1 004_energymin]$ ls
+O86.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan1 004_energymin]$ cd ../005_dock/rigid/
+(base) [ehspector@milan1 rigid]$ ls
+rigid.in  rigid.sh
+(base) [ehspector@milan1 rigid]$ vi rigid.sh
+(base) [ehspector@milan1 rigid]$ bash rigid.sh
+(base) [ehspector@milan1 rigid]$ ls
+rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
+(base) [ehspector@milan1 rigid]$ vi rigid.out
+(base) [ehspector@milan1 rigid]$ grep -c "Name" rigid_scored.mol2
+(base) [ehspector@milan1 rigid]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cd ../../
+(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.in 1O86/005_dock/fixed_anchor/fad.in
+(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.sh 1O86/005_dock/fixed_anchor/fad.sh
+(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.in 1O86/005_dock/flex/flex.in
+(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.sh 1O86/005_dock/flex/flex.sh
+(base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/fixed_anchor/
+(base) [ehspector@milan1 fixed_anchor]$ ls
+fad.in  fad.sh
+(base) [ehspector@milan1 fixed_anchor]$ vi fad.in
+(base) [ehspector@milan1 fixed_anchor]$ bash fad.sh
+(base) [ehspector@milan1 fixed_anchor]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cd fixed_anchor/
+(base) [ehspector@milan1 fixed_anchor]$ ls
+fad.in  fad.out  fad_scored.mol2  fad.sh
+(base) [ehspector@milan1 fixed_anchor]$ grep -c "Name" fad_scored.mol2
+(base) [ehspector@milan1 fixed_anchor]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cd flex/
+(base) [ehspector@milan1 flex]$ ls
+flex.in  flex.sh
+(base) [ehspector@milan1 flex]$ vi flex.in
+(base) [ehspector@milan1 flex]$ bash flex.sh
+^C^X
+(base) [ehspector@milan1 flex]$ vi flex.in
+(base) [ehspector@milan1 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan1 flex]$ rm flex.out
+(base) [ehspector@milan1 flex]$ bash flex.sh
+(base) [ehspector@milan1 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan1 flex]$ vi flex.out
+(base) [ehspector@milan1 flex]$ grep -c "Name" flex_scored.mol2
+(base) [ehspector@milan1 flex]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/005_dock/flex_docking/
+(base) [ehspector@milan1 flex_docking]$ vi flex.in
+(base) [ehspector@milan1 flex_docking]$ cd ..
+(base) [ehspector@milan1 005_dock]$ cd ../../5EEN/005_dock/flex/
+(base) [ehspector@milan1 flex]$ vi flex.in
+(base) [ehspector@milan1 flex]$ exit
+(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+****IMPORTANT MESSAGE BELOW****
+In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/
+(base) [ehspector@login2 install]$ ls
+bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
+bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
+config.h   gnu.parallel        ibmaix                   Makefile        test
+configure  gnu.parallel.rdkit  intel                    oneapi
+docker     gnu.rdkit           intel.intelmpi.parallel  pgi
+gnu        gnu.valgrind        intel.ip.mkl             rules.h
+(base) [ehspector@login2 install]$ ./configure gnu
+The requested configuration file was found.
+Warning: the configuration file already exists with the creation stamp:
+# Created at Mon Jan 20 04:34:02 PM EST 2025 via ./configure gnu.rdkit
+It will be overwritten !
+Don't forget to make clean before rebuilding.
+To reconfigure and rebuild everything start with make -i distclean:
+Reconfiguring after make -i distclean will avoid this warning.
+The DOCK configuration file has been created.
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Wed Feb 12 10:29:40 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
+g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
+g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
+g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
+g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
+g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
+g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
+g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
+g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
+g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
+g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
+g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
+g++ -c -O2 -std=c++11 -o score.o  score.cpp
+g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
+g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
+g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
+g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
+g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
+g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
+g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
+g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
+g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
+g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
+g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
+g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
+g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
+g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
+g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
+g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
+g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
+cd nab && make all
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-lm -lpthread
+mv dock6 ../../bin
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Wed Feb 12 10:31:34 EST 2025.
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ..
+(base) [ehspector@login2 src]$ cd ../install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Wed Feb 12 10:33:23 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:550:9: error: ‘num_zeros’ was not declared in this scope
+|     if (num_zeros == mol.num_atoms){
+      |         ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+make[1]: *** [dockmol.o] Error 1
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [dock] Error 2
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ../
+(base) [ehspector@login2 src]$ cd ../install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Wed Feb 12 10:36:16 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
+g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
+g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
+g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
+g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
+g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
+g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
+g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
+g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
+g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
+g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
+g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
+g++ -c -O2 -std=c++11 -o score.o  score.cpp
+g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
+g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
+g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
+g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
+g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
+g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
+g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
+g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
+g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
+g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
+g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
+g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
+g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
+g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
+g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
+g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
+g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
+cd nab && make all
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-lm -lpthread
+mv dock6 ../../bin
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Wed Feb 12 10:38:00 EST 2025.
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd ,,
+-bash: cd: ,,: No such file or directory
+(base) [ehspector@login2 alpha_branch]$ home
+(base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2   gas_4.in               gas.in               no_gas.out_scored.mol2
+AAQ_yesG.mol2  gas_4.out              gas.out              test.mol2
+gas_2.in        gas_4.out_scored.mol2  gas.out_scored.mol2  test_nocharge.mol2
+gas_2.out       gas_5.in               no_charge
+gas_3.in        gas_5.out              no_gas.in
+gas_3.out       gas_5.out_scored.mol2  no_gas.out
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.out
+(base) [ehspector@login2 gas_teiger]$ rm gas_4.out
+(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas.out
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2   gas_3.out              gas_5.out_scored.mol2  no_gas.in
+AAQ_yesG.mol2  gas_4.in               gas.in                 no_gas.out
+gas_2.in        gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+gas_2.out       gas_5.in               gas.out_scored.mol2    test.mol2
+gas_3.in        gas_5.out              no_charge              test_nocharge.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.out
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login2 gas_teiger]$ vi gas_5.in
+(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2
+(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2
+(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_5.in -o gas_5.out
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2   gas_3.out              gas_5.out_scored.mol2  no_gas.in
+AAQ_yesG.mol2  gas_4.in               gas.in                 no_gas.out
+gas_2.in        gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+gas_2.out       gas_5.in               gas.out_scored.mol2    test.mol2
+gas_3.in        gas_5.out              no_charge              test_nocharge.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_5.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_5.in
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2   gas_4.in               gas.in               no_gas.out_scored.mol2
+AAQ_yesG.mol2  gas_4.out              gas.out              test.mol2
+gas_2.in        gas_4.out_scored.mol2  gas.out_scored.mol2  test_nocharge.mol2
+gas_2.out       gas_5.in               no_charge
+gas_3.in        gas_5.out              no_gas.in
+gas_3.out       gas_5.out_scored.mol2  no_gas.out
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.out
+(base) [ehspector@login2 gas_teiger]$ cd ..
+(base) [ehspector@login2 4s0v]$ cd ..
+(base) [ehspector@login2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@login2 dock]$ vi filter.cpp
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ..
+(base) [ehspector@login2 src]$ cd ../install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Wed Feb 12 10:49:54 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:542:5: error: ‘If’ was not declared in this scope
+|     If all partial charges are zero, it is a bad molecule
+      |     ^~
+dockmol.cpp:546:13: error: ‘num_zeros’ was not declared in this scope
+|             num_zeros += 1;
+      |             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp:549:6: error: ‘Is’ was not declared in this scope
+|      Is it a bad molecule?
+      |      ^~
+dockmol.cpp:552:7: error: ‘else’ without a previous ‘if’
+|     } else {
+      |       ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+make[1]: *** [dockmol.o] Error 1
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [dock] Error 2
+(base) [ehspector@login2 install]$ cd ../src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ..
+(base) [ehspector@login2 src]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd src/dock
+(base) [ehspector@login2 dock]$ cd ../../
+(base) [ehspector@login2 alpha_branch]$ cd install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Wed Feb 12 10:52:33 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
+g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
+g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
+g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
+g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
+g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
+g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
+g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
+g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
+g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
+g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
+g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
+g++ -c -O2 -std=c++11 -o score.o  score.cpp
+g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
+g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
+g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
+g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
+g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
+g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
+g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
+g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
+g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
+g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
+g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
+g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
+g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
+g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
+g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
+g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
+g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
+cd nab && make all
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-lm -lpthread
+mv dock6 ../../bin
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Wed Feb 12 10:54:21 EST 2025.
+(base) [ehspector@login2 install]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+****IMPORTANT MESSAGE BELOW****
+In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
+(base) [ehspector@login1 ~]$ home
+(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
+(base) [ehspector@login1 src]$ ls
+accessories  antechamber  dock  docktools  gbsa_grids  grid  Makefile  mopac6  rdkit  resp  tleap
+(base) [ehspector@login1 src]$ cd dock
+(base) [ehspector@login1 dock]$ ls
+amber_typer.cpp     defreal.h        iso_align.o           README                score.o
+amber_typer.h       dock.cpp         library_file.cpp      sasa.cpp              score_ph4.cpp
+amber_typer.o       dockmol.cpp      library_file.h        sasa.h                score_ph4.h
+base_grid.cpp       dockmol.h        library_file.o        sasa.o                score_ph4.o
+base_grid.h         dockmol.o        limit_max_change.cpp  score_amber.cpp       score_sasa.cpp
+base_grid.o         dock.o           limit_max_change.h    score_amber.h         score_sasa.h
+base_mpi.cpp        filter.cpp       limit_max_change.o    score_amber.o         score_sasa.o
+base_mpi.h          filter.h         lol                   score_chemgrid.cpp    score_solvent.cpp
+base_mpi.o          filter.o         Makefile              score_chemgrid.h      score_solvent.h
+base_score.cpp      fingerprint.cpp  master_conf.cpp       score_chemgrid.o      score_solvent.o
+base_score.h        fingerprint.h    master_conf.h         score.cpp             score_volume.cpp
+base_score.o        fingerprint.o    master_conf.o         score_descriptor.cpp  score_volume.h
+conf_gen_ag.cpp     fraggraph.cpp    master_score.cpp      score_descriptor.h    score_volume.o
+conf_gen_ag.h       fraggraph.h      master_score.h        score_descriptor.o    simplex.cpp
+conf_gen_ag.o       fraggraph.o      master_score.o        score_footprint.cpp   simplex.h
+conf_gen_cg.cpp     fragment.cpp     mem_info.cpp          score_footprint.h     simplex.o
+conf_gen_cg.h       fragment.h       mem_info.h            score_footprint.o     sphere.cpp
+conf_gen_cg.o       fragment.o       mem_info.o            score_gist.cpp        sphere.h
+conf_gen_dn.cpp     gasteiger.cpp    nab                   score_gist.h          sphere.o
+conf_gen_dn_ga.cpp  gasteiger.h      nabcode.h             score_gist.o          tnt
+conf_gen_dn_ga.h    gasteiger.o      nab.h                 score.h               trace.cpp
+conf_gen_dn_ga.o    grid.cpp         orient.cpp            score_hbond.cpp       trace.h
+conf_gen_dn.h       grid.h           orient.h              score_hbond.h         trace.inl
+conf_gen_dn.o       grid.o           orient.o              score_hbond.o         trace.o
+conf_gen_ga.cpp     gzstream         rddrive.cpp           score_internal.cpp    utils.cpp
+conf_gen_ga.h       hungarian.cpp    rddrive.h             score_internal.h      utils.h
+conf_gen_ga.o       hungarian.h      rddrive.o             score_internal.o      utils.o
+conf_gen_hdb.cpp    hungarian.o      rdtyper.cpp           score_multigrid.cpp   version.h
+conf_gen_hdb.h      iso_align.cpp    rdtyper.h             score_multigrid.h     xlogp.cpp
+conf_gen_hdb.o      iso_align.h      rdtyper.o             score_multigrid.o     xlogp.h
+(base) [ehspector@login1 dock]$ vi dockmol.cpp
+(base) [ehspector@login1 dock]$ cd ../../install/
+(base) [ehspector@login1 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login1 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Wed Feb 12 13:24:37 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
+g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
+g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
+g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
+g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
+g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
+g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
+g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
+g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
+g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
+g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
+g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
+g++ -c -O2 -std=c++11 -o score.o  score.cpp
+g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
+g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
+g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
+g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
+g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
+g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
+g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
+g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
+g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
+g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
+g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
+g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
+g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
+g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
+g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
+g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
+g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
+cd nab && make all
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-lm -lpthread
+mv dock6 ../../bin
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Wed Feb 12 13:27:09 EST 2025.
+(base) [ehspector@login1 install]$ cd ..
+(base) [ehspector@login1 alpha_branch]$ cd ../../4s0v/gas_teiger/
+(base) [ehspector@login1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_3.out              gas_5.out              no_charge               test_nocharge.mol2
+AAQ_yesG.mol2  gas_4.in               gas_5.out_scored.mol2  no_gas.in
+gas_2.in        gas_4.out              gas.in                 no_gas.out
+gas_2.out       gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+gas_3.in        gas_5.in               gas.out_scored.mol2    test.mol2
+(base) [ehspector@login1 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@login1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_3.out              gas_5.out              no_charge               test_nocharge.mol2
+AAQ_yesG.mol2  gas_4.in               gas_5.out_scored.mol2  no_gas.in
+gas_2.in        gas_4.out              gas.in                 no_gas.out
+gas_2.out       gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+gas_3.in        gas_5.in               gas.out_scored.mol2    test.mol2
+(base) [ehspector@login1 gas_teiger]$ vi 1AAQ_noG.mol2
+(base) [ehspector@login1 gas_teiger]$ vi gas_4.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ vi gas_3.in
+(base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2
+(base) [ehspector@login1 gas_teiger]$ vi gas_3.in
+(base) [ehspector@login1 gas_teiger]$ vi gas_3.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out
+(base) [ehspector@login1 gas_teiger]$ vi gas_3.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2
+(base) [ehspector@login1 gas_teiger]$ vi test.mol2
+(base) [ehspector@login1 gas_teiger]$ vi  gas_2.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@login1 gas_teiger]$ ls
+AAQ_noG.mol2   gas_3.out              gas_5.in               gas.out_scored.mol2     test.mol2
+AAQ_yesG.mol2  gas_3.out_scored.mol2  gas_5.out              no_charge               test_nocharge.mol2
+gas_2.in        gas_4.in               gas_5.out_scored.mol2  no_gas.in
+gas_2.out       gas_4.out              gas.in                 no_gas.out
+gas_3.in        gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ vi gas_2.in
+(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
+(base) [ehspector@login1 gas_teiger]$ vi gas_2.out_scored.mol2
+(base) [ehspector@login1 gas_teiger]$ cd ..
+(base) [ehspector@login1 4s0v]$ cd ../../
+(base) [ehspector@login1 rizzo]$ home
+(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
+accessories/ dock/        gbsa_grids/  mopac6/      resp/
+antechamber/ docktools/   grid/        rdkit/       tleap/
+(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
+accessories/ dock/        gbsa_grids/  mopac6/      resp/
+antechamber/ docktools/   grid/        rdkit/       tleap/
+(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
+accessories/ dock/        gbsa_grids/  mopac6/      resp/
+antechamber/ docktools/   grid/        rdkit/       tleap/
+(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@login1 dock]$ vi dockmol.cpp
+\(base) [ehspector@login1 dock]$ vi filter.cpp
+(base) [ehspector@login1 dock]$ vi library_file.cpp
+(base) [ehspector@login1 dock]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP 5EEN % ls
+een.lig.min_scored.mol2	5een_noH_nocH.mol2
+een.pdb			5een_protein_only.pdb
+een.sph			5een_surface.dms
+een_H_cH.mol2			fad_scored.mol2
+een_ligand_H_cH.mol2		flex_scored.mol2
+een_ligand_noH_nocH.mol2	rigid_scored.mol2
+een_ligand_only.pdb		selected_spheres.sph
+(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 1O86]$ cd 005_dock/
+(base) [ehspector@milan2 005_dock]$ cd rigid/
+(base) [ehspector@milan2 rigid]$ ls
+rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
+(base) [ehspector@milan2 rigid]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
+(base) [ehspector@milan2 flex]$ vi flex.out
+(base) [ehspector@milan2 flex]$ vi flex.in
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ rm flex.out
+(base) [ehspector@milan2 flex]$ bash flex.sh
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ vi flex.out
+(base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ vi flex.sh
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ ls
+flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
+(base) [ehspector@milan2 flex]$ which dock6
+/gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6
+(base) [ehspector@milan2 flex]$ vi ~/.bashrc
+(base) [ehspector@milan2 flex]$ cd ..
+(base) [ehspector@milan2 005_dock]$ cd ..
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        004_energymin          007_cartesian_min  Notes.txt
+_surface_spheres  005_dock               008_rescore        Robs_2w26
+_gridbox          006_virtual_screening  commands.txt       test4.tar
+(base) [ehspector@milan2 2w26]$ cd 004_energymin/
+(base) [ehspector@milan2 004_energymin]$ ls
+w26.lig.min_scored.mol2  min.in  min.out  min.sh
+(base) [ehspector@milan2 004_energymin]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        004_energymin          007_cartesian_min  Notes.txt
+_surface_spheres  005_dock               008_rescore        Robs_2w26
+_gridbox          006_virtual_screening  commands.txt       test4.tar
+(base) [ehspector@milan2 2w26]$ mv 006_virtual_screening/ 006_footprint
+(base) [ehspector@milan2 2w26]$ ls
+_structure        004_energymin  007_cartesian_min  Notes.txt
+_surface_spheres  005_dock       008_rescore        Robs_2w26
+_gridbox          006_footprint  commands.txt       test4.tar
+(base) [ehspector@milan2 2w26]$ cd 006_footprint/
+(base) [ehspector@milan2 006_footprint]$ touch footprint.in
+(base) [ehspector@milan2 006_footprint]$ ls
+footprint.in
+(base) [ehspector@milan2 006_footprint]$ cd ..
+(base) [ehspector@milan2 2w26]$ cp 003_gridbox/grid.sh 006_footprint/foot.sh
+(base) [ehspector@milan2 2w26]$ cd 006_footprint/
+(base) [ehspector@milan2 006_footprint]$ vi foot.sh
+(base) [ehspector@milan2 006_footprint]$ vi foot.sh
+(base) [ehspector@milan2 006_footprint]$ class
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ cd class_project/
+(base) [ehspector@milan2 class_project]$ ls
+(base) [ehspector@milan2 class_project]$ ls
+(base) [ehspector@milan2 class_project]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        004_energymin  007_cartesian_min  Notes.txt
+_surface_spheres  005_dock       008_rescore        Robs_2w26
+_gridbox          006_footprint  commands.txt       test4.tar
+(base) [ehspector@milan2 2w26]$ mv Notes.txt ../../
+(base) [ehspector@milan2 2w26]$ mv commands.txt ../../
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox    005_dock       007_cartesian_min  Robs_2w26
+_surface_spheres  004_energymin  006_footprint  008_rescore        test4.tar
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan2 AMS_536]$ vi commands.txt
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        003_gridbox    005_dock       007_cartesian_min  Robs_2w26
+_surface_spheres  004_energymin  006_footprint  008_rescore        test4.tar
+(base) [ehspector@milan2 2w26]$ mkdir 007_virtual_screen
+(base) [ehspector@milan2 2w26]$ ls
+_structure        004_energymin  007_cartesian_min   Robs_2w26
+_surface_spheres  005_dock       007_virtual_screen  test4.tar
+_gridbox          006_footprint  008_rescore
+(base) [ehspector@milan2 2w26]$ mv 007_cartesian_min/ 008_cartesian_min
+(base) [ehspector@milan2 2w26]$ mv 008_rescore/  009_rescore
+(base) [ehspector@milan2 2w26]$ cd ../5EEN/
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 5EEN]$ mv 006_virtual_screen_mpi/ 006_footprint
+(base) [ehspector@milan2 5EEN]$ mkdir 007_virtualscreen
+(base) [ehspector@milan2 5EEN]$ mv 007_cartesian_min/ 008_cartesian_min
+(base) [ehspector@milan2 5EEN]$ mv 008_rescore/ 009_rescore
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
+(base) [ehspector@milan2 5EEN]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 1O86
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
+_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
+(base) [ehspector@milan2 1O86]$ mv 006_virtual_screen_mpi/ 006_footprint
+(base) [ehspector@milan2 1O86]$ mkdir 007_virtualscreen
+(base) [ehspector@milan2 1O86]$ mv 007_cartesian_min/ 008_cartesian_min
+(base) [ehspector@milan2 1O86]$ mv 008_rescore/ 009_rescore
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ vi commands.txt
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ bash commands.txt
+commands.txt: line 2: protein_name: Is a directory
+commands.txt: line 3: protein_name: Is a directory
+commands.txt: line 4: protein_name: Is a directory
+commands.txt: line 5: protein_name: Is a directory
+commands.txt: line 6: protein_name: Is a directory
+commands.txt: line 10: protein_name: Is a directory
+commands.txt: line 11: protein_name: Is a directory
+commands.txt: line 12: protein_name: Is a directory
+commands.txt: line 13: protein_name: Is a directory
+(base) [ehspector@milan2 AMS_536]$ ls
+_dock       commands.txt  flex       protein_name  Tutorials
+class_project  fixed_anchor  Notes.txt  rigid
+(base) [ehspector@milan2 AMS_536]$ cd protein_name/
+(base) [ehspector@milan2 protein_name]$ ls
+(base) [ehspector@milan2 protein_name]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ rm protein_name/
+rm: cannot remove 'protein_name/': Is a directory
+(base) [ehspector@milan2 AMS_536]$ rm -r protein_name/
+(base) [ehspector@milan2 AMS_536]$ rm 005_dock
+(base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
+(base) [ehspector@milan2 AMS_536]$ rm -r flex/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  rigid  Tutorials
+(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ vi commands.txt
+(base) [ehspector@milan2 AMS_536]$ bash commands.txt
+(base) [ehspector@milan2 AMS_536]$ ls
+_structure        005_dock           009_rescore    flex          Tutorials
+_surface_spheres  006_footprint      class_project  Notes.txt
+_gridbox          007_virtualscreen  commands.txt   protein_name
+_energymin        008_cartesian_min  fixed_anchor   rigid
+(base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/
+(base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/
+(base) [ehspector@milan2 AMS_536]$ rm -r 003_surface_spheres/
+rm: cannot remove '003_surface_spheres/': No such file or directory
+(base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/
+(base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/
+(base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/
+(base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/
+(base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/
+(base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/
+(base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/
+(base) [ehspector@milan2 AMS_536]$ rm -r protein_name/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  fixed_anchor  flex  Notes.txt  rigid  Tutorials
+(base) [ehspector@milan2 AMS_536]$ rm -r flex
+(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
+(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
+rm: cannot remove 'rigid/': No such file or directory
+(base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
+(base) [ehspector@milan2 AMS_536]$ rm -r flex
+rm: cannot remove 'flex': No such file or directory
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ vi commands.txt
+(base) [ehspector@milan2 AMS_536]$ bash commands.txt
+mkdir: cannot create directory ‘protein_name’: File exists
+mkdir: cannot create directory ‘protein_name’: File exists
+(base) [ehspector@milan2 AMS_536]$ ls
+_structure        005_dock           009_rescore    flex          Tutorials
+_surface_spheres  006_footprint      class_project  Notes.txt
+_gridbox          007_virtualscreen  commands.txt   protein_name
+_energymin        008_cartesian_min  fixed_anchor   rigid
+(base) [ehspector@milan2 AMS_536]$ rm -r flex
+(base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
+(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
+(base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/
+(base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/
+(base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/
+(base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/
+(base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/
+(base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/
+(base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/
+(base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/
+(base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  protein_name  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd protein_name/
+(base) [ehspector@milan2 protein_name]$ ls
+(base) [ehspector@milan2 protein_name]$ cd ..
+(base) [ehspector@milan2 AMS_536]$ sinfo
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      4    mix a100-[03-05,11]
+a100                      up    8:00:00      3  alloc a100-[06,08,10]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      4    mix a100-[03-05,11]
+a100-large                up    8:00:00      3  alloc a100-[06,08,10]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
+a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
+debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+debug-40core              up    1:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+extended-40core           up 7-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+extended-40core-shared    up 3-12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+extended-96core           up 7-00:00:00      1    mix dg023
+extended-96core           up 7-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+extended-96core-shared    up 3-12:00:00      1    mix dg023
+extended-96core-shared    up 3-12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
+hbm-1tb-long-96core       up 2-00:00:00      2  alloc xm[045,047]
+hbm-1tb-long-96core       up 2-00:00:00      1   idle xm046
+hbm-extended-96core       up 7-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+large-40core              up    8:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+large-96core              up    8:00:00      1    mix dg023
+large-96core              up    8:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+long-40core               up 2-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+long-40core-shared        up 1-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+long-96core               up 2-00:00:00      1    mix dg023
+long-96core               up 2-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+long-96core-shared        up 1-00:00:00      1    mix dg023
+long-96core-shared        up 1-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+medium-40core             up   12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+medium-96core             up   12:00:00      1    mix dg023
+medium-96core             up   12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+short-40core              up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+short-40core-shared       up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+short-96core              up    4:00:00      1    mix dg023
+short-96core              up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+short-96core-shared       up    4:00:00      1    mix dg023
+short-96core-shared       up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  protein_name  Tutorials
+(base) [ehspector@milan2 AMS_536]$ rm -r protein_name
+(base) [ehspector@milan2 AMS_536]$ vi ~/.bashrc
+(base) [ehspector@milan2 AMS_536]$ source ~/.bashrc
+(base) [ehspector@milan2 AMS_536]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      4    mix a100-[03-05,11]
+a100                      up    8:00:00      3  alloc a100-[06,08,10]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      4    mix a100-[03-05,11]
+a100-large                up    8:00:00      3  alloc a100-[06,08,10]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
+a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
+debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+debug-40core              up    1:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+extended-40core           up 7-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+extended-40core-shared    up 3-12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+extended-96core           up 7-00:00:00      1    mix dg023
+extended-96core           up 7-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+extended-96core-shared    up 3-12:00:00      1    mix dg023
+extended-96core-shared    up 3-12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
+hbm-1tb-long-96core       up 2-00:00:00      1  alloc xm047
+hbm-1tb-long-96core       up 2-00:00:00      2   idle xm[045-046]
+hbm-extended-96core       up 7-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+large-40core              up    8:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+large-96core              up    8:00:00      1    mix dg023
+large-96core              up    8:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+long-40core               up 2-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+long-40core-shared        up 1-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+long-96core               up 2-00:00:00      1    mix dg023
+long-96core               up 2-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+long-96core-shared        up 1-00:00:00      1    mix dg023
+long-96core-shared        up 1-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+medium-40core             up   12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+medium-96core             up   12:00:00      1    mix dg023
+medium-96core             up   12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+short-40core              up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
+short-40core-shared       up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+short-96core              up    4:00:00      1    mix dg023
+short-96core              up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
+short-96core-shared       up    4:00:00      1    mix dg023
+short-96core-shared       up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
+(base) [ehspector@milan2 AMS_536]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+(base) [ehspector@milan2 AMS_536]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP 5EEN % ls
+een.lig.min_scored.mol2	5een_noH_nocH.mol2
+een.pdb			5een_protein_only.pdb
+een.sph			5een_surface.dms
+een_H_cH.mol2			fad_scored.mol2
+een_ligand_H_cH.mol2		flex_scored.mol2
+een_ligand_noH_nocH.mol2	rigid_scored.mol2
+een_ligand_only.pdb		selected_spheres.sph
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ home
+(base) [ehspector@milan1 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan1 espector]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/006_footprint/
+(base) [ehspector@milan1 006_footprint]$ ls
+footprint.in  foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd
+(base) [ehspector@milan1 ~]$ cd ../../
+(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/2025/transfers/
+(base) [ehspector@milan1 transfers]$ ls
+_02_12a_test.tar
+(base) [ehspector@milan1 transfers]$ cd ..
+(base) [ehspector@milan1 2025]$ ls
+EVE_DOCK_VS  additional_files  INSPH  robbashrc_file  rotations  transfers
+(base) [ehspector@milan1 2025]$ cd transfers/
+(base) [ehspector@milan1 transfers]$ pwd
+/gpfs/projects/AMS536/2025/transfers
+(base) [ehspector@milan1 transfers]$ ^C
+(base) [ehspector@milan1 transfers]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/transfers/2025_02_12a_test.tar .
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2025_02_12a_test.tar  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ mv 2025_02_12a_test.tar 2w26/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        003_gridbox    005_dock       007_virtual_screen  009_rescore           Robs_2w26
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min   2025_02_12a_test.tar  test4.tar
+(base) [ehspector@milan1 2w26]$ tar -xf 2025_02_12a_test.tar
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   2W26
+_gridbox          006_footprint  009_rescore         Robs_2w26
+(base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan1 Robs_new_2w26]$ ls
+_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
+(base) [ehspector@milan1 005_analysis]$ ls
+fps_footprint_scored.txt      01fps_hbond_scored.txt  01fps.log1  01fps.out          01fps.sh
+fps_footprint_scored.txt.pdf  01fps.in                01fps.log2  01fps_scored.mol2
+(base) [ehspector@milan1 005_analysis]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/005_analysis/01fps.in 006_footprint/footprint.in
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/005_analysis/
+(base) [ehspector@milan1 005_analysis]$ vi 01fps
+(base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
+(base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
+(base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
+(base) [ehspector@milan1 005_analysis]$ cd ../../006_footprint/
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ vi footprint.sh
+(base) [ehspector@milan1 006_footprint]$ ls
+footprint.in  foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ cd ../001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+w26_ligand_H_cH.mol2  2w26_ligand_noH_nocH.mol2  2w26_protein_H_cH.mol2  2w26_protein_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/2w26.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/2w26_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/2w26_protein_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        footprint
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+-----------------------------------
+Molecule: 2w26.pdb
+ Elapsed time for docking:	0.008 seconds
+ Anchors:		1
+ Orientations:		1
+ Conformations:		1
+          Footprint_Similarity_Score:            0.761241
+                      FPS_vdw_energy:          -76.920898
+                       FPS_es_energy:           -2.930423
+                   FPS_vdw+es_energy:          -79.851318
+                       FPS_num_hbond:                   2
+                         FPS_vdw_fps:            0.642335
+                          FPS_es_fps:            0.118906
+                          FPS_hb_fps:            0.000000
+                   FPS_vdw_fp_numres:                 286
+                    FPS_es_fp_numres:                 286
+                    FPS_hb_fp_numres:                 286
+Molecules Processed
+Total elapsed time:	0.587 seconds
+Number of molecules per second:	1.705
+Virtual memory used for this process: 80220 kilobytes
+Physical memory used for this process: 8192 kilobytes
+Traceback (most recent call last):
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 9, in <module>
+    import matplotlib
+ModuleNotFoundError: No module named 'matplotlib'
+(base) [ehspector@milan1 006_footprint]$ module load python
+(base) [ehspector@milan1 006_footprint]$ module list
+Currently Loaded Modulefiles:
+) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack
+) shared                   4) mvapich2/gcc13.2/2.3.7   6) python/3.11.2
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/2w26.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/2w26_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/2w26_protein_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        footprint
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+-----------------------------------
+Molecule: 2w26.pdb
+ Elapsed time for docking:	0.008 seconds
+ Anchors:		1
+ Orientations:		1
+ Conformations:		1
+          Footprint_Similarity_Score:            0.761241
+                      FPS_vdw_energy:          -76.920898
+                       FPS_es_energy:           -2.930423
+                   FPS_vdw+es_energy:          -79.851318
+                       FPS_num_hbond:                   2
+                         FPS_vdw_fps:            0.642335
+                          FPS_es_fps:            0.118906
+                          FPS_hb_fps:            0.000000
+                   FPS_vdw_fp_numres:                 286
+                    FPS_es_fp_numres:                 286
+                    FPS_hb_fp_numres:                 286
+Molecules Processed
+Total elapsed time:	0.487 seconds
+Number of molecules per second:	2.053
+Virtual memory used for this process: 80224 kilobytes
+Physical memory used for this process: 8192 kilobytes
+Traceback (most recent call last):
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
+    main()
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
+    (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
+                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
+    fp_file = open(filename,'r')
+              ^^^^^^^^^^^^^^^^^^
+FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt'
+(base) [ehspector@milan1 006_footprint]$ ls
+footprint_footprint_scored.txt  footprint_hbond_scored.txt  footprint.in  footprint_scored.mol2  foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/2w26.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/2w26_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/2w26_protein_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        2w26
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+-----------------------------------
+Molecule: 2w26.pdb
+ Elapsed time for docking:	0.008 seconds
+ Anchors:		1
+ Orientations:		1
+ Conformations:		1
+          Footprint_Similarity_Score:            0.761241
+                      FPS_vdw_energy:          -76.920898
+                       FPS_es_energy:           -2.930423
+                   FPS_vdw+es_energy:          -79.851318
+                       FPS_num_hbond:                   2
+                         FPS_vdw_fps:            0.642335
+                          FPS_es_fps:            0.118906
+                          FPS_hb_fps:            0.000000
+                   FPS_vdw_fp_numres:                 286
+                    FPS_es_fp_numres:                 286
+                    FPS_hb_fp_numres:                 286
+Molecules Processed
+Total elapsed time:	0.525 seconds
+Number of molecules per second:	1.905
+Virtual memory used for this process: 80224 kilobytes
+Physical memory used for this process: 8192 kilobytes
+Traceback (most recent call last):
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
+    main()
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
+    (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
+                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
+    fp_file = open(filename,'r')
+              ^^^^^^^^^^^^^^^^^^
+FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt'
+(base) [ehspector@milan1 006_footprint]$ ls
+w26_footprint_scored.txt  footprint_footprint_scored.txt  footprint_scored.mol2
+w26_hbond_scored.txt      footprint_hbond_scored.txt      foot.sh
+w26_scored.mol2           footprint.in
+(base) [ehspector@milan1 006_footprint]$ rm *mol2
+(base) [ehspector@milan1 006_footprint]$ ls
+w26_footprint_scored.txt  footprint_footprint_scored.txt  footprint.in
+w26_hbond_scored.txt      footprint_hbond_scored.txt      foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ rm *.txt
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/2w26.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/2w26_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/2w26_protein_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        2w26
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+-----------------------------------
+Molecule: 2w26.pdb
+ Elapsed time for docking:	0.008 seconds
+ Anchors:		1
+ Orientations:		1
+ Conformations:		1
+          Footprint_Similarity_Score:            0.761241
+                      FPS_vdw_energy:          -76.920898
+                       FPS_es_energy:           -2.930423
+                   FPS_vdw+es_energy:          -79.851318
+                       FPS_num_hbond:                   2
+                         FPS_vdw_fps:            0.642335
+                          FPS_es_fps:            0.118906
+                          FPS_hb_fps:            0.000000
+                   FPS_vdw_fp_numres:                 286
+                    FPS_es_fp_numres:                 286
+                    FPS_hb_fp_numres:                 286
+Molecules Processed
+Total elapsed time:	0.585 seconds
+Number of molecules per second:	1.710
+Virtual memory used for this process: 80224 kilobytes
+Physical memory used for this process: 8192 kilobytes
+No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
+/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
+  plt.show()
+(base) [ehspector@milan1 006_footprint]$ ls
+w26_footprint_scored.txt      2w26_hbond_scored.txt  footprint.in
+w26_footprint_scored.txt.pdf  2w26_scored.mol2       foot.sh
+(base) [ehspector@milan1 006_footprint]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan1 Robs_new_2w26]$ ls
+_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
+(base) [ehspector@milan1 005_analysis]$ ls
+fps_footprint_scored.txt      01fps_hbond_scored.txt  01fps.log1  01fps.out          01fps.sh
+fps_footprint_scored.txt.pdf  01fps.in                01fps.log2  01fps_scored.mol2
+(base) [ehspector@milan1 005_analysis]$ cd ../006_ga_lib/
+(base) [ehspector@milan1 006_ga_lib]$ ls
+lib.sh                  2W26.fraglib.out             2W26_fragout_scored.mol2
+combine.sh              2W26_fraglib_rigid.mol2      full_fraglib.dat
+W26.fraglib.in           2W26_fraglib_scaffold.mol2   full_sorted_fraglib.dat
+W26_fraglib_linker.mol2  2W26_fraglib_sidechain.mol2  unique_full_sorted_fraglib.dat
+W26.fraglib.log          2W26_fraglib_torenv.dat
+(base) [ehspector@milan1 006_ga_lib]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan1 Robs_new_2w26]$ ls
+_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 000_test/
+(base) [ehspector@milan1 000_test]$ ls
+test_dock.in
+(base) [ehspector@milan1 000_test]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/
+(base) [ehspector@milan1 004_dock]$ ls
+min.in           02rgd.in           03fad.in           04flx.in   05vs.out
+min.log          02rgd.log          03fad.log          04flx.log  05vs_scored.mol2
+min.out          02rgd.out          03fad.out          04flx.out  05vs.sh
+min_scored.mol2  02rgd_scored.mol2  03fad_scored.mol2  04flx.sh   05vs_slurm
+min.sh           02rgd.sh           03fad.sh           05vs.in    VS_library_005.mol2
+(base) [ehspector@milan1 004_dock]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/004_dock/05vs.in 007_virtual_screen/
+(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+vs.in
+(base) [ehspector@milan1 007_virtual_screen]$ mv 05vs.in virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ cd
+(base) [ehspector@milan1 ~]$ cd ../../
+(base) [ehspector@milan1 gpfs]$ cd AMS536
+-bash: cd: AMS536: No such file or directory
+(base) [ehspector@milan1 gpfs]$ cd projects/AMS536
+(base) [ehspector@milan1 AMS536]$ ls
+EVE_Lig_nH.mol2    1eve_Rec_nH.mol2  2018  2021  2024            junk.txt
+EVE_Lig_wH.mol2    1eve_Rec_wH.mol2  2019  2022  2025            zzz.anchors
+EVE_Rec_nHDMS.dms  2017              2020  2023  get_anchors.py  zzz.programs
+(base) [ehspector@milan1 AMS536]$ cd 2025
+(base) [ehspector@milan1 2025]$ cd ..
+(base) [ehspector@milan1 AMS536]$ cd zzz.programs/
+(base) [ehspector@milan1 zzz.programs]$ ls
+amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
+de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
+dock6.10         dock6.12         gen-frags-12         VS_libraries
+dock6.10_milan   dock6.12_ams536  old
+(base) [ehspector@milan1 zzz.programs]$ cd VS_libraries/
+(base) [ehspector@milan1 VS_libraries]$ ls
+VS_library_100.mol2  VS_library_25K.mol2  VS_library_5K.mol2
+(base) [ehspector@milan1 VS_libraries]$ pwd
+/gpfs/projects/AMS536/zzz.programs/VS_libraries
+(base) [ehspector@milan1 VS_libraries]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ cd ../006_footprint/
+(base) [ehspector@milan1 006_footprint]$ ls
+w26_footprint_scored.txt      2w26_hbond_scored.txt  footprint.in
+w26_footprint_scored.txt.pdf  2w26_scored.mol2       foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ cd ../007_virtual_screen/
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
+(base) [ehspector@milan1 007_virtual_screen]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan1 Robs_new_2w26]$ ls
+_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
+(base) [ehspector@milan1 005_analysis]$ ls
+fps_footprint_scored.txt      01fps_hbond_scored.txt  01fps.log1  01fps.out          01fps.sh
+fps_footprint_scored.txt.pdf  01fps.in                01fps.log2  01fps_scored.mol2
+(base) [ehspector@milan1 005_analysis]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/
+(base) [ehspector@milan1 004_dock]$ ls
+min.in           02rgd.in           03fad.in           04flx.in   05vs.out
+min.log          02rgd.log          03fad.log          04flx.log  05vs_scored.mol2
+min.out          02rgd.out          03fad.out          04flx.out  05vs.sh
+min_scored.mol2  02rgd_scored.mol2  03fad_scored.mol2  04flx.sh   05vs_slurm
+min.sh           02rgd.sh           03fad.sh           05vs.in    VS_library_005.mol2
+(base) [ehspector@milan1 004_dock]$ vi 05vs.sh
+(base) [ehspector@milan1 004_dock]$ vi 05vs.sh
+(base) [ehspector@milan1 004_dock]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+virtual.in  virtual.slurm
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
+(base) [ehspector@milan1 007_virtual_screen]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      4    mix a100-[03-05,11]
+a100                      up    8:00:00      3  alloc a100-[06,08,10]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      4    mix a100-[03-05,11]
+a100-large                up    8:00:00      3  alloc a100-[06,08,10]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
+a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
+debug-40core              up    1:00:00      3   plnd dn[032,040,049]
+debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      8    mix dn[001,003-005,007,018,027,051]
+debug-40core              up    1:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+extended-40core           up 7-00:00:00      3   plnd dn[032,040,049]
+extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      8    mix dn[001,003-005,007,018,027,051]
+extended-40core           up 7-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+extended-40core-shared    up 3-12:00:00      3   plnd dn[032,040,049]
+extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      8    mix dn[001,003-005,007,018,027,051]
+extended-40core-shared    up 3-12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+extended-96core           up 7-00:00:00      1    mix dg023
+extended-96core           up 7-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+extended-96core-shared    up 3-12:00:00      1    mix dg023
+extended-96core-shared    up 3-12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
+hbm-1tb-long-96core       up 2-00:00:00      1  alloc xm045
+hbm-1tb-long-96core       up 2-00:00:00      2   idle xm[046-047]
+hbm-extended-96core       up 7-00:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      3   plnd dn[032,040,049]
+large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      8    mix dn[001,003-005,007,018,027,051]
+large-40core              up    8:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+large-96core              up    8:00:00      1    mix dg023
+large-96core              up    8:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+long-40core               up 2-00:00:00      3   plnd dn[032,040,049]
+long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      8    mix dn[001,003-005,007,018,027,051]
+long-40core               up 2-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+long-40core-shared        up 1-00:00:00      3   plnd dn[032,040,049]
+long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      8    mix dn[001,003-005,007,018,027,051]
+long-40core-shared        up 1-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+long-96core               up 2-00:00:00      1    mix dg023
+long-96core               up 2-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+long-96core-shared        up 1-00:00:00      1    mix dg023
+long-96core-shared        up 1-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+medium-40core             up   12:00:00      3   plnd dn[032,040,049]
+medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      8    mix dn[001,003-005,007,018,027,051]
+medium-40core             up   12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+medium-96core             up   12:00:00      1    mix dg023
+medium-96core             up   12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+ood-short-96core          up    4:00:00      1  alloc dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      3   plnd dn[032,040,049]
+short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
+short-40core              up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+short-40core-shared       up    4:00:00      3   plnd dn[032,040,049]
+short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
+short-40core-shared       up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+short-96core              up    4:00:00      1    mix dg023
+short-96core              up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+short-96core-shared       up    4:00:00      1    mix dg023
+short-96core-shared       up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+virtual.in  virtual.slurm
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
+(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.slurm
+sbatch: error: QOSMaxNodePerJobLimit
+sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+(base) [ehspector@milan1 007_virtual_screen]$ mv virtual.slurm virtual.sh
+(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
+sbatch: error: QOSMaxNodePerJobLimit
+sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
+Submitted batch job 927425
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan1 007_virtual_screen]$
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan1 007_virtual_screen]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan1 ~]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      4    mix a100-[03-05,11]
+a100                      up    8:00:00      3  alloc a100-[06,08,10]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      4    mix a100-[03-05,11]
+a100-large                up    8:00:00      3  alloc a100-[06,08,10]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
+a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
+debug-40core              up    1:00:00      3   plnd dn[032,040,049]
+debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      8    mix dn[001,003-005,007,018,027,051]
+debug-40core              up    1:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+extended-40core           up 7-00:00:00      3   plnd dn[032,040,049]
+extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      8    mix dn[001,003-005,007,018,027,051]
+extended-40core           up 7-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+extended-40core-shared    up 3-12:00:00      3   plnd dn[032,040,049]
+extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      8    mix dn[001,003-005,007,018,027,051]
+extended-40core-shared    up 3-12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+extended-96core           up 7-00:00:00      1    mix dg023
+extended-96core           up 7-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+extended-96core-shared    up 3-12:00:00      1    mix dg023
+extended-96core-shared    up 3-12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
+hbm-1tb-long-96core       up 2-00:00:00      1  alloc xm045
+hbm-1tb-long-96core       up 2-00:00:00      2   idle xm[046-047]
+hbm-extended-96core       up 7-00:00:00      2   plnd xm[008,094]
+hbm-extended-96core       up 7-00:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
+hbm-large-96core          up    8:00:00      2   plnd xm[008,094]
+hbm-large-96core          up    8:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
+hbm-long-96core           up 2-00:00:00      2   plnd xm[008,094]
+hbm-long-96core           up 2-00:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
+hbm-medium-96core         up   12:00:00      2   plnd xm[008,094]
+hbm-medium-96core         up   12:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
+hbm-short-96core          up    4:00:00      2   plnd xm[008,094]
+hbm-short-96core          up    4:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
+large-40core              up    8:00:00      3   plnd dn[032,040,049]
+large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      8    mix dn[001,003-005,007,018,027,051]
+large-40core              up    8:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+large-96core              up    8:00:00      1    mix dg023
+large-96core              up    8:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+long-40core               up 2-00:00:00      3   plnd dn[032,040,049]
+long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      8    mix dn[001,003-005,007,018,027,051]
+long-40core               up 2-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+long-40core-shared        up 1-00:00:00      3   plnd dn[032,040,049]
+long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      8    mix dn[001,003-005,007,018,027,051]
+long-40core-shared        up 1-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+long-96core               up 2-00:00:00      1    mix dg023
+long-96core               up 2-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+long-96core-shared        up 1-00:00:00      1    mix dg023
+long-96core-shared        up 1-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+medium-40core             up   12:00:00      3   plnd dn[032,040,049]
+medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      8    mix dn[001,003-005,007,018,027,051]
+medium-40core             up   12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+medium-96core             up   12:00:00      1    mix dg023
+medium-96core             up   12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      3   plnd dn[032,040,049]
+short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
+short-40core              up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+short-40core-shared       up    4:00:00      3   plnd dn[032,040,049]
+short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
+short-40core-shared       up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+short-96core              up    4:00:00      1    mix dg023
+short-96core              up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
+short-96core-shared       up    4:00:00      1    mix dg023
+short-96core-shared       up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
+(base) [ehspector@milan1 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan1 2w26]$ scancel 927425
+(base) [ehspector@milan1 2w26]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+virtual.in  virtual.sh
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
+Submitted batch job 927435
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 007_virtual_screen]$ cd ..
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 5EEN/006_footprint/footprint.in
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 5EEN/006_footprint/foot.sh
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 1O86/006_footprint/foot.sh
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 1O86/006_footprint/footprint.in
+(base) [ehspector@milan1 Tutorials]$ cd 5EEN/006_footprint/
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ module load python
+(base) [ehspector@milan1 006_footprint]$ cd ../001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/5een.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/5een_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/5een_protein_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        5een
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+Error Opening Receptor File!
+Traceback (most recent call last):
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
+    main()
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
+    (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
+                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 56, in identify_residues
+    resindex_selected.append(fp_array[(num_res-1)-i][0])
+:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])^^^^^^^^^^^^^^^
+IndexError: list index out of range
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/5een.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/5een_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/5een_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        5een
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 3018
+WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5500
+WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5501
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type K in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+-----------------------------------
+Molecule: 5een.pdb
+ Elapsed time for docking:	0.008 seconds
+ Anchors:		1
+ Orientations:		1
+ Conformations:		1
+          Footprint_Similarity_Score:           10.378089
+                      FPS_vdw_energy:          -39.542568
+                       FPS_es_energy:          -11.422824
+                   FPS_vdw+es_energy:          -50.965393
+                       FPS_num_hbond:                   2
+                         FPS_vdw_fps:            8.225544
+                          FPS_es_fps:            2.152545
+                          FPS_hb_fps:            0.000000
+                   FPS_vdw_fp_numres:                 362
+                    FPS_es_fp_numres:                 362
+                    FPS_hb_fp_numres:                 362
+Molecules Processed
+Total elapsed time:	0.778 seconds
+Number of molecules per second:	1.285
+Virtual memory used for this process: 80616 kilobytes
+Physical memory used for this process: 9196 kilobytes
+No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
+/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
+  plt.show()
+(base) [ehspector@milan1 006_footprint]$ ls
+een_footprint_scored.txt      5een_hbond_scored.txt  footprint.in
+een_footprint_scored.txt.pdf  5een_scored.mol2       foot.sh
+(base) [ehspector@milan1 006_footprint]$ cd ..
+(base) [ehspector@milan1 5EEN]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd 1O86/001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+O86_ligand_H_cH.mol2  1O86_ligand_noH_nocH.mol2  1O86_protein_H_cH.mol2  1O86_protein_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
+(base) [ehspector@milan1 006_footprint]$ vi footprint.in
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ vi foot.sh
+(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+conformer_search_type                                        rigid
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+use_internal_energy                                          no
+Molecule Library Input Parameters
+------------------------------------------------------------------------------------------
+ligand_atom_file                                             ../004_energymin/1O86.lig.min_scored.mol2
+limit_max_ligands                                            no
+skip_molecule                                                no
+read_mol_solvation                                           no
+calculate_rmsd                                               no
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+use_database_filter                                          no
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+orient_ligand                                                no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+bump_filter                                                  no
+Master Score Parameters
+------------------------------------------------------------------------------------------
+score_molecules                                              yes
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+contact_score_primary                                        no
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+grid_score_primary                                           no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+gist_score_primary                                           no
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+multigrid_score_primary                                      no
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+dock3.5_score_primary                                        no
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+continuous_score_primary                                     no
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+footprint_similarity_score_primary                           yes
+fps_score_use_footprint_reference_mol2                       yes
+fps_score_footprint_reference_mol2_filename                  ../001_structure/1O86_ligand_H_cH.mol2
+fps_score_foot_compare_type                                  Euclidean
+-------------------------------------------------------------
+You chose to use the Euclidean distance as the metric
+to compare the footprints.  When the value is 0 then
+there is perfect agreement between the two footprints.
+As the agreement gets worse between the two
+footprints the value increases.
+-------------------------------------------------------------
+fps_score_normalize_foot                                     no
+fps_score_foot_comp_all_residue                              yes
+fps_score_receptor_filename                                  ../001_structure/1O86_protein_H_cH.mol2
+fps_score_vdw_att_exp                                        6
+fps_score_vdw_rep_exp                                        9
+fps_score_vdw_rep_rad_scale                                  1
+fps_score_use_distance_dependent_dielectric                  yes
+fps_score_dielectric                                         4.0
+fps_score_vdw_fp_scale                                       1
+fps_score_es_fp_scale                                        1
+fps_score_hb_fp_scale                                        0
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+minimize_ligand                                              no
+simplex_final_min                                            no
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+Molecule Library Output Parameters
+------------------------------------------------------------------------------------------
+ligand_outfile_prefix                                        1O86
+write_mol_solvation                                          no
+write_footprints                                             yes
+write_hbonds                                                 yes
+write_orientations                                           no
+num_scored_conformers                                        1
+score_threshold                                              100.0
+rank_ligands                                                 no
+------------------------------------------------------------------------------------------
+Initializing Library File Routines...
+To cite Footprint Similarity Score use:
+ Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+Warning: atom type Zn in Fingerprint::return_atom_type not recognized
+-----------------------------------
+Molecule: 1O86_ligand.pdb
+ Elapsed time for docking:	0.019 seconds
+ Anchors:		1
+ Orientations:		1
+ Conformations:		1
+          Footprint_Similarity_Score:           19.990522
+                      FPS_vdw_energy:          -62.449921
+                       FPS_es_energy:          -49.059299
+                   FPS_vdw+es_energy:         -111.509216
+                       FPS_num_hbond:                   4
+                         FPS_vdw_fps:            4.596808
+                          FPS_es_fps:           15.393714
+                          FPS_hb_fps:            1.000000
+                   FPS_vdw_fp_numres:                 582
+                    FPS_es_fp_numres:                 582
+                    FPS_hb_fp_numres:                 582
+Molecules Processed
+Total elapsed time:	2.107 seconds
+Number of molecules per second:	0.475
+Virtual memory used for this process: 83536 kilobytes
+Physical memory used for this process: 11424 kilobytes
+No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
+/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
+  plt.show()
+(base) [ehspector@milan1 006_footprint]$ ls
+O86_footprint_scored.txt      1O86_hbond_scored.txt  footprint.in
+O86_footprint_scored.txt.pdf  1O86_scored.mol2       foot.sh
+(base) [ehspector@milan1 006_footprint]$ cd ..
+(base) [ehspector@milan1 1O86]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 5EEN/007_virtualscreen/virtual.in
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 5EEN/007_virtualscreen/virtual.sh
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 1O86/007_virtualscreen/virtual.sh
+(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 1O86/007_virtualscreen/virtual.in
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan2 ~]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      2    mix a100-[03,05]
+a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      2    mix a100-[03,05]
+a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      2    mix a100-[03,05]
+a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
+debug-40core              up    1:00:00      3   plnd dn[050,061-062]
+debug-40core              up    1:00:00      6 alloc@ dn[009,026,029,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      4    mix dn[004-005,018,051]
+debug-40core              up    1:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+extended-40core           up 7-00:00:00      3   plnd dn[050,061-062]
+extended-40core           up 7-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      4    mix dn[004-005,018,051]
+extended-40core           up 7-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+extended-40core-shared    up 3-12:00:00      3   plnd dn[050,061-062]
+extended-40core-shared    up 3-12:00:00      6 alloc@ dn[009,026,029,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      4    mix dn[004-005,018,051]
+extended-40core-shared    up 3-12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core           up 7-00:00:00      2    mix dg[009,023]
+extended-96core           up 7-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+extended-96core           up 7-00:00:00      3   idle dg[032,035-036]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
+extended-96core-shared    up 3-12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+extended-96core-shared    up 3-12:00:00      3   idle dg[032,035-036]
+hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
+hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
+hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      3   plnd dn[050,061-062]
+large-40core              up    8:00:00      6 alloc@ dn[009,026,029,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      4    mix dn[004-005,018,051]
+large-40core              up    8:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+large-96core              up    8:00:00      2    mix dg[009,023]
+large-96core              up    8:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+large-96core              up    8:00:00      3   idle dg[032,035-036]
+long-40core               up 2-00:00:00      3   plnd dn[050,061-062]
+long-40core               up 2-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      4    mix dn[004-005,018,051]
+long-40core               up 2-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+long-40core-shared        up 1-00:00:00      3   plnd dn[050,061-062]
+long-40core-shared        up 1-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      4    mix dn[004-005,018,051]
+long-40core-shared        up 1-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core               up 2-00:00:00      2    mix dg[009,023]
+long-96core               up 2-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+long-96core               up 2-00:00:00      3   idle dg[032,035-036]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
+long-96core-shared        up 1-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+long-96core-shared        up 1-00:00:00      3   idle dg[032,035-036]
+medium-40core             up   12:00:00      3   plnd dn[050,061-062]
+medium-40core             up   12:00:00      6 alloc@ dn[009,026,029,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      4    mix dn[004-005,018,051]
+medium-40core             up   12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+medium-96core             up   12:00:00      2    mix dg[009,023]
+medium-96core             up   12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+medium-96core             up   12:00:00      3   idle dg[032,035-036]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      3   plnd dn[050,061-062]
+short-40core              up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      4    mix dn[004-005,018,051]
+short-40core              up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+short-40core-shared       up    4:00:00      3   plnd dn[050,061-062]
+short-40core-shared       up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      4    mix dn[004-005,018,051]
+short-40core-shared       up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core              up    4:00:00      2    mix dg[009,023]
+short-96core              up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+short-96core              up    4:00:00      3   idle dg[032,035-036]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core-shared       up    4:00:00      2    mix dg[009,023]
+short-96core-shared       up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
+short-96core-shared       up    4:00:00      3   idle dg[032,035-036]
+(base) [ehspector@milan2 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
+(base) [ehspector@milan2 ~]$ scancel 927435
+(base) [ehspector@milan2 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh
+Submitted batch job 928050
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtual_screen]$ scancel 928050
+(base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh
+Submitted batch job 928053
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       0:03      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       0:07      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       0:10      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       0:49      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtual_screen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       0:50      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtual_screen]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       1:42      3 dg[032,035-036]
+(base) [ehspector@milan2 Tutorials]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       1:43      3 dg[032,035-036]
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/
+(base) [ehspector@milan2 006_footprint]$ ls
+w26_footprint_scored.txt      2w26_hbond_scored.txt  footprint.in
+w26_footprint_scored.txt.pdf  2w26_scored.mol2       foot.sh
+(base) [ehspector@milan2 006_footprint]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       6:28      3 dg[032,035-036]
+(base) [ehspector@milan2 006_footprint]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       6:29      3 dg[032,035-036]
+(base) [ehspector@milan2 006_footprint]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       6:56      3 dg[032,035-036]
+(base) [ehspector@milan2 006_footprint]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R       7:42      3 dg[032,035-036]
+(base) [ehspector@milan2 006_footprint]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ../5EEN/
+(base) [ehspector@milan2 5EEN]$ ls
+_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
+(base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
+(base) [ehspector@milan2 007_virtualscreen]$ ls
+virtual.in  virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      2    mix a100-[03,05]
+a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      2    mix a100-[03,05]
+a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      2    mix a100-[03,05]
+a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
+debug-40core              up    1:00:00      3   plnd dn[050,061-062]
+debug-40core              up    1:00:00      6 alloc@ dn[009,026,029,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      4    mix dn[004-005,018,051]
+debug-40core              up    1:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+extended-40core           up 7-00:00:00      3   plnd dn[050,061-062]
+extended-40core           up 7-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      4    mix dn[004-005,018,051]
+extended-40core           up 7-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+extended-40core-shared    up 3-12:00:00      3   plnd dn[050,061-062]
+extended-40core-shared    up 3-12:00:00      6 alloc@ dn[009,026,029,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      4    mix dn[004-005,018,051]
+extended-40core-shared    up 3-12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+extended-96core           up 7-00:00:00      1   plnd dg039
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core           up 7-00:00:00      2    mix dg[009,023]
+extended-96core           up 7-00:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+extended-96core-shared    up 3-12:00:00      1   plnd dg039
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
+extended-96core-shared    up 3-12:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
+hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
+hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      3   plnd dn[050,061-062]
+large-40core              up    8:00:00      6 alloc@ dn[009,026,029,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      4    mix dn[004-005,018,051]
+large-40core              up    8:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+large-96core              up    8:00:00      1   plnd dg039
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+large-96core              up    8:00:00      2    mix dg[009,023]
+large-96core              up    8:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+long-40core               up 2-00:00:00      3   plnd dn[050,061-062]
+long-40core               up 2-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      4    mix dn[004-005,018,051]
+long-40core               up 2-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+long-40core-shared        up 1-00:00:00      3   plnd dn[050,061-062]
+long-40core-shared        up 1-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      4    mix dn[004-005,018,051]
+long-40core-shared        up 1-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+long-96core               up 2-00:00:00      1   plnd dg039
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core               up 2-00:00:00      2    mix dg[009,023]
+long-96core               up 2-00:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+long-96core-shared        up 1-00:00:00      1   plnd dg039
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
+long-96core-shared        up 1-00:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+medium-40core             up   12:00:00      3   plnd dn[050,061-062]
+medium-40core             up   12:00:00      6 alloc@ dn[009,026,029,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      4    mix dn[004-005,018,051]
+medium-40core             up   12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+medium-96core             up   12:00:00      1   plnd dg039
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+medium-96core             up   12:00:00      2    mix dg[009,023]
+medium-96core             up   12:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      3   plnd dn[050,061-062]
+short-40core              up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      4    mix dn[004-005,018,051]
+short-40core              up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+short-40core-shared       up    4:00:00      3   plnd dn[050,061-062]
+short-40core-shared       up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      4    mix dn[004-005,018,051]
+short-40core-shared       up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
+short-96core              up    4:00:00      1   plnd dg039
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core              up    4:00:00      2    mix dg[009,023]
+short-96core              up    4:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+short-96core-shared       up    4:00:00      1   plnd dg039
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core-shared       up    4:00:00      2    mix dg[009,023]
+short-96core-shared       up    4:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.in
+(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928057
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      12:28      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      12:41      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      12:46      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      12:47      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      12:49      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      14:35      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      14:38      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      14:40      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      14:42      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ ls
+virtual.in  virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      15:00      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      15:06      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ scancel 928057
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_vs_ ehspecto  R      16:00      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      2    mix a100-[03,05]
+a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      2    mix a100-[03,05]
+a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      2    mix a100-[03,05]
+a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
+debug-40core              up    1:00:00      2   plnd dn[061-062]
+debug-40core              up    1:00:00      6 alloc@ dn[009,026,029,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      4    mix dn[004-005,018,051]
+debug-40core              up    1:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+extended-40core           up 7-00:00:00      2   plnd dn[061-062]
+extended-40core           up 7-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      4    mix dn[004-005,018,051]
+extended-40core           up 7-00:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+extended-40core-shared    up 3-12:00:00      2   plnd dn[061-062]
+extended-40core-shared    up 3-12:00:00      6 alloc@ dn[009,026,029,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      4    mix dn[004-005,018,051]
+extended-40core-shared    up 3-12:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+extended-96core           up 7-00:00:00      3   plnd dg[006,026,039]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core           up 7-00:00:00      2    mix dg[009,023]
+extended-96core           up 7-00:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+extended-96core-shared    up 3-12:00:00      3   plnd dg[006,026,039]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
+extended-96core-shared    up 3-12:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
+hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
+hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      2   plnd dn[061-062]
+large-40core              up    8:00:00      6 alloc@ dn[009,026,029,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      4    mix dn[004-005,018,051]
+large-40core              up    8:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+large-96core              up    8:00:00      3   plnd dg[006,026,039]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+large-96core              up    8:00:00      2    mix dg[009,023]
+large-96core              up    8:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+long-40core               up 2-00:00:00      2   plnd dn[061-062]
+long-40core               up 2-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      4    mix dn[004-005,018,051]
+long-40core               up 2-00:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+long-40core-shared        up 1-00:00:00      2   plnd dn[061-062]
+long-40core-shared        up 1-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      4    mix dn[004-005,018,051]
+long-40core-shared        up 1-00:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+long-96core               up 2-00:00:00      3   plnd dg[006,026,039]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core               up 2-00:00:00      2    mix dg[009,023]
+long-96core               up 2-00:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+long-96core-shared        up 1-00:00:00      3   plnd dg[006,026,039]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
+long-96core-shared        up 1-00:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+medium-40core             up   12:00:00      2   plnd dn[061-062]
+medium-40core             up   12:00:00      6 alloc@ dn[009,026,029,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      4    mix dn[004-005,018,051]
+medium-40core             up   12:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+medium-96core             up   12:00:00      3   plnd dg[006,026,039]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+medium-96core             up   12:00:00      2    mix dg[009,023]
+medium-96core             up   12:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      2   plnd dn[061-062]
+short-40core              up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      4    mix dn[004-005,018,051]
+short-40core              up    4:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+short-40core-shared       up    4:00:00      2   plnd dn[061-062]
+short-40core-shared       up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      4    mix dn[004-005,018,051]
+short-40core-shared       up    4:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
+short-96core              up    4:00:00      3   plnd dg[006,026,039]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core              up    4:00:00      2    mix dg[009,023]
+short-96core              up    4:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+short-96core-shared       up    4:00:00      3   plnd dg[006,026,039]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core-shared       up    4:00:00      2    mix dg[009,023]
+short-96core-shared       up    4:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
+(base) [ehspector@milan2 007_virtualscreen]$ cd ../
+(base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928060
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
+short-96c 2w26_vs_ ehspecto  R      19:15      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
+short-96c 2w26_vs_ ehspecto  R      19:17      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
+short-96c 2w26_vs_ ehspecto  R      19:18      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
+short-96c 2w26_vs_ ehspecto  R      19:19      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      19:38      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      19:40      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      19:41      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928063
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
+short-96c 2w26_vs_ ehspecto  R      21:35      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ scancel 928063
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      21:54      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
+sbatch: error: QOSMaxNodePerJobLimit
+sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928066
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:11      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:13      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:13      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:16      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:17      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:17      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      23:18      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      24:32      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      24:38      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      24:39      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928070
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      25:10      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 2w26_vs_ ehspecto  R      25:19      3 dg[032,035-036]
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+(base) [ehspector@milan2 007_virtualscreen]$ scancel 928066
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      25:37      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      25:50      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 2w26_vs_ ehspecto  R      25:51      3 dg[032,035-036]
+(base) [ehspector@milan2 007_virtualscreen]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@login.seawulf.stonybrook.edu
+ehspector@login.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+****IMPORTANT MESSAGE BELOW****
+In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
+(base) [ehspector@login2 ~]$ cd ..
+(base) [ehspector@login2 home]$ home
+(base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ../../install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+amake[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock\
+> ^C
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Thu Feb 13 11:05:05 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:778:5: error: ‘Filter’ was not declared in this scope
+|     Filter filter;
+      |     ^12:36, 21 February 2025 (EST)
+make[1]: *** [dockmol.o] Error 1
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [dock] Error 2
+(base) [ehspector@login2 install]$ cd ../../
+(base) [ehspector@login2 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ../../
+(base) [ehspector@login2 alpha_branch]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+(base) [ehspector@login2 alpha_branch]$ cd install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Thu Feb 13 11:07:50 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
+g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
+g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
+g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
+g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
+g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
+g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
+g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
+g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
+g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
+g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
+g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
+g++ -c -O2 -std=c++11 -o score.o  score.cpp
+g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
+g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
+g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
+g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
+g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
+g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
+g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
+g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
+g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
+g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
+g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
+g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
+g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
+g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
+g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
+g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
+g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
+cd nab && make all
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-lm -lpthread
+mv dock6 ../../bin
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+(base) [ehspector@login2 install]$ cd ../
+(base) [ehspector@login2 alpha_branch]$ cd ../
+(base) [ehspector@login2 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ..
+(base) [ehspector@login2 src]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Thu Feb 13 11:20:49 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘gasteiger’; did you mean ‘gasteigerize’?
+|     if (filter.gasteiger){
+      |                ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+      |                gasteigerize
+dockmol.cpp:931:5: error: jump to label ‘skip’
+|     skip:
+      |     ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp:918:10: note:   from here
+|     goto skip;
+      |          ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp:919:9: note:   crosses initialization of ‘int num_zeros’
+|     int num_zeros = 0;
+      |         ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+make[1]: *** [dockmol.o] Error 1
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [dock] Error 2
+(base) [ehspector@login2 install]$ cd ..
+(base) [ehspector@login2 alpha_branch]$ cd src/dock
+(base) [ehspector@login2 dock]$ vi dockmol.cpp
+(base) [ehspector@login2 dock]$ cd ..
+\(base) [ehspector@login2 src]$ cd ../
+(base) [ehspector@login2 alpha_branch]$ cd install/
+(base) [ehspector@login2 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@login2 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Thu Feb 13 11:25:35 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
+g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
+g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
+g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
+g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
+g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
+g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
+g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
+g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
+g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
+g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
+g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
+g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
+g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
+g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
+g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
+g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
+g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
+g++ -c -O2 -std=c++11 -o score.o  score.cpp
+g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
+g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
+g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
+g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
+g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
+g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
+g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
+g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
+g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
+g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
+g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
+g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
+g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
+g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
+g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
+g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
+g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
+cd nab && make all
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-lm -lpthread
+mv dock6 ../../bin
+make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Thu Feb 13 11:27:30 EST 2025.
+(base) [ehspector@login2 install]$ cd
+(base) [ehspector@login2 ~]$ home
+(base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2          gas_3.out              gas_5.out              no_gas.in
+AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out_scored.mol2  no_gas.out
+gas_2.in               gas_4.in               gas.in                 no_gas.out_scored.mol2
+gas_2.out              gas_4.out              gas.out                test.mol2
+gas_2.out_scored.mol2  gas_4.out_scored.mol2  gas.out_scored.mol2    test_nocharge.mol2
+gas_3.in               gas_5.in               no_charge
+(base) [ehspector@login2 gas_teiger]$ mkdir test
+(base) [ehspector@login2 gas_teiger]$ vi gas_3.in
+(base) [ehspector@login2 gas_teiger]$ mv test_nocharge.mol2 test
+(base) [ehspector@login2 gas_teiger]$ mv gas_3.in
+mv: missing destination file operand after ‘gas_3.in’
+Try 'mv --help' for more information.
+(base) [ehspector@login2 gas_teiger]$ mv gas_3.in test
+(base) [ehspector@login2 gas_teiger]$ cd test/
+(base) [ehspector@login2 test]$ ls
+gas_3.in  test_nocharge.mol2
+(base) [ehspector@login2 test]$ vi test_nocharge.mol2
+(base) [ehspector@login2 test]$ vi gas_3.in
+(base) [ehspector@login2 test]$ dock6 -i gas_3.in -o gas_3.out
+(base) [ehspector@login2 test]$ ls
+gas_3.in  gas_3.out  gas_3.out_scored.mol2  test_nocharge.mol2
+(base) [ehspector@login2 test]$ vi gas_3.out
+(base) [ehspector@login2 test]$ vi gas_3.out_scored.mol2
+(base) [ehspector@login2 test]$ vi gas_3.out
+(base) [ehspector@login2 test]$ cd ..
+(base) [ehspector@login2 gas_teiger]$ cd ..
+(base) [ehspector@login2 4s0v]$ cd gas_teiger/
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2          gas_3.out              gas_5.in               gas.out_scored.mol2     test
+AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out              no_charge               test.mol2
+gas_2.in               gas_4.in               gas_5.out_scored.mol2  no_gas.in
+gas_2.out              gas_4.out              gas.in                 no_gas.out
+gas_2.out_scored.mol2  gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
+(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@login2 gas_teiger]$ ls
+AAQ_noG.mol2          gas_3.out              gas_5.in               gas.out_scored.mol2     test
+AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out              no_charge               test.mol2
+gas_2.in               gas_4.in               gas_5.out_scored.mol2  no_gas.in
+gas_2.out              gas_4.out              gas.in                 no_gas.out
+gas_2.out_scored.mol2  gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2
+(base) [ehspector@login2 gas_teiger]$ cd ..
+(base) [ehspector@login2 4s0v]$ cd gas_teiger/
+(base) [ehspector@login2 gas_teiger]$ mv gas_4.in test
+(base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2
+mv: missing destination file operand after ‘1AAQ_noG.mol2’
+Try 'mv --help' for more information.
+(base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2 test
+(base) [ehspector@login2 gas_teiger]$ home
+(base) [ehspector@login2 espector]$ rd
+srun: error: invalid partition specified: short-40core
+srun: error: Unable to allocate resources: Invalid partition name specified
+(base) [ehspector@login2 espector]$ exit
+logout
+Connection to login.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ rd
+srun: job 928167 queued and waiting for resources
+^Csrun: Job allocation 928167 has been revoked
+srun: Force Terminated job 928167
+(base) [ehspector@milan1 ~]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       0:23      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:11:38      3 dg[032,035-036]
+(base) [ehspector@milan1 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       0:30      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:11:45      3 dg[032,035-036]
+(base) [ehspector@milan1 ~]$ cd ..
+(base) [ehspector@milan1 home]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/1O86/007_virtualscreen/
+(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtualscreen]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      1   mix@ a100-02
+a100                      up    8:00:00      2 alloc@ a100-[07,09]
+a100                      up    8:00:00      1 drain* a100-01
+a100                      up    8:00:00      2    mix a100-[03,05]
+a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-large                up    8:00:00      1   mix@ a100-02
+a100-large                up    8:00:00      2 alloc@ a100-[07,09]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      2    mix a100-[03,05]
+a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
+a100-long                 up 2-00:00:00      1   mix@ a100-02
+a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      2    mix a100-[03,05]
+a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
+debug-40core              up    1:00:00      6   plnd dn[024-025,054,056-058]
+debug-40core              up    1:00:00      5 alloc@ dn[026,029,035,038,045]
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      5    mix dn[004-005,018,051,061]
+debug-40core              up    1:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+extended-40core           up 7-00:00:00      6   plnd dn[024-025,054,056-058]
+extended-40core           up 7-00:00:00      5 alloc@ dn[026,029,035,038,045]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      5    mix dn[004-005,018,051,061]
+extended-40core           up 7-00:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+extended-40core-shared    up 3-12:00:00      6   plnd dn[024-025,054,056-058]
+extended-40core-shared    up 3-12:00:00      5 alloc@ dn[026,029,035,038,045]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      5    mix dn[004-005,018,051,061]
+extended-40core-shared    up 3-12:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+extended-96core           up 7-00:00:00      1   mix@ dg040
+extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core           up 7-00:00:00      2    mix dg[009,023]
+extended-96core           up 7-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+extended-96core           up 7-00:00:00      3   idle dg[042,046-047]
+extended-96core-shared    up 3-12:00:00      1   mix@ dg040
+extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
+extended-96core-shared    up 3-12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+extended-96core-shared    up 3-12:00:00      3   idle dg[042,046-047]
+hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
+hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
+hbm-extended-96core       up 7-00:00:00      3   plnd xm[003,006-007]
+hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-extended-96core       up 7-00:00:00      1  drain xm017
+hbm-extended-96core       up 7-00:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-large-96core          up    8:00:00      3   plnd xm[003,006-007]
+hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-large-96core          up    8:00:00      1  drain xm017
+hbm-large-96core          up    8:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-long-96core           up 2-00:00:00      3   plnd xm[003,006-007]
+hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-long-96core           up 2-00:00:00      1  drain xm017
+hbm-long-96core           up 2-00:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-medium-96core         up   12:00:00      3   plnd xm[003,006-007]
+hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-medium-96core         up   12:00:00      1  drain xm017
+hbm-medium-96core         up   12:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
+hbm-short-96core          up    4:00:00      3   plnd xm[003,006-007]
+hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
+hbm-short-96core          up    4:00:00      1  drain xm017
+hbm-short-96core          up    4:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
+large-40core              up    8:00:00      6   plnd dn[024-025,054,056-058]
+large-40core              up    8:00:00      5 alloc@ dn[026,029,035,038,045]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      5    mix dn[004-005,018,051,061]
+large-40core              up    8:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+large-96core              up    8:00:00      1   mix@ dg040
+large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+large-96core              up    8:00:00      2    mix dg[009,023]
+large-96core              up    8:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+large-96core              up    8:00:00      3   idle dg[042,046-047]
+long-40core               up 2-00:00:00      6   plnd dn[024-025,054,056-058]
+long-40core               up 2-00:00:00      5 alloc@ dn[026,029,035,038,045]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      5    mix dn[004-005,018,051,061]
+long-40core               up 2-00:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+long-40core-shared        up 1-00:00:00      6   plnd dn[024-025,054,056-058]
+long-40core-shared        up 1-00:00:00      5 alloc@ dn[026,029,035,038,045]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      5    mix dn[004-005,018,051,061]
+long-40core-shared        up 1-00:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+long-96core               up 2-00:00:00      1   mix@ dg040
+long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core               up 2-00:00:00      2    mix dg[009,023]
+long-96core               up 2-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+long-96core               up 2-00:00:00      3   idle dg[042,046-047]
+long-96core-shared        up 1-00:00:00      1   mix@ dg040
+long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
+long-96core-shared        up 1-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+long-96core-shared        up 1-00:00:00      3   idle dg[042,046-047]
+medium-40core             up   12:00:00      6   plnd dn[024-025,054,056-058]
+medium-40core             up   12:00:00      5 alloc@ dn[026,029,035,038,045]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      5    mix dn[004-005,018,051,061]
+medium-40core             up   12:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+medium-96core             up   12:00:00      1   mix@ dg040
+medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+medium-96core             up   12:00:00      2    mix dg[009,023]
+medium-96core             up   12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+medium-96core             up   12:00:00      3   idle dg[042,046-047]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      6   plnd dn[024-025,054,056-058]
+short-40core              up    4:00:00      5 alloc@ dn[026,029,035,038,045]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      5    mix dn[004-005,018,051,061]
+short-40core              up    4:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+short-40core-shared       up    4:00:00      6   plnd dn[024-025,054,056-058]
+short-40core-shared       up    4:00:00      5 alloc@ dn[026,029,035,038,045]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      5    mix dn[004-005,018,051,061]
+short-40core-shared       up    4:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
+short-96core              up    4:00:00      1   mix@ dg040
+short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core              up    4:00:00      2    mix dg[009,023]
+short-96core              up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+short-96core              up    4:00:00      3   idle dg[042,046-047]
+short-96core-shared       up    4:00:00      1   mix@ dg040
+short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
+short-96core-shared       up    4:00:00      2    mix dg[009,023]
+short-96core-shared       up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
+short-96core-shared       up    4:00:00      3   idle dg[042,046-047]
+(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.in
+(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928174
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       3:06      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:14:21      3 dg[032,035-036]
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       3:49      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:15:04      3 dg[032,035-036]
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       3:52      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:15:07      3 dg[032,035-036]
+(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh
+Submitted batch job 928179
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 1O86_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 5een_vs_ ehspecto  R       4:21      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:15:36      3 dg[032,035-036]
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 1O86_vs_ ehspecto PD       0:00      3 (Priority)
+short-96c 5een_vs_ ehspecto  R       4:22      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:15:37      3 dg[032,035-036]
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       4:55      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:16:10      3 dg[032,035-036]
+short-96c 1O86_vs_ ehspecto  R       0:24      3 dg[026,046-047]
+(base) [ehspector@milan1 007_virtualscreen]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R       5:47      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:17:02      3 dg[032,035-036]
+short-96c 1O86_vs_ ehspecto  R       1:16      3 dg[026,046-047]
+(base) [ehspector@milan1 007_virtualscreen]$ home
+(base) [ehspector@milan1 espector]$ rd
+srun: job 928192 queued and waiting for resources
+srun: job 928192 has been allocated resources
+(base) [ehspector@dn050 espector]$ cd builds/alpha_branch/install/
+(base) [ehspector@dn050 install]$ ls
+bluegenel  docker    gnu.parallel        homebrew        intel.intelmpi.parallel  Makefile  sgi
+bluegenep  gnu       gnu.parallel.rdkit  homebrew.rdkit  intel.ip.mkl             oneapi    sgi.parallel
+config.h   gnu.acml  gnu.rdkit           ibmaix          intel.mkl                pgi       test
+configure  gnu.gdb   gnu.valgrind        intel           intel.parallel           rules.h
+(base) [ehspector@dn050 install]$ configure gnu.rdkit
+bash: configure: command not found
+(base) [ehspector@dn050 install]$ ./configure gnu.rdkit
+The requested configuration file was found.
+Warning: the configuration file already exists with the creation stamp:
+# Created at Wed Feb 12 10:29:31 EST 2025 via ./configure gnu
+It will be overwritten !
+Don't forget to make clean before rebuilding.
+To reconfigure and rebuild everything start with make -i distclean:
+Reconfiguring after make -i distclean will avoid this warning.
+The DOCK configuration file has been created.
+ REQUIREMENTS - define these environment variables
+ RDBASE is the root directory of RDKit
+ BOOST is the root directory of Boost
+(base) [ehspector@dn050 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn050 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Thu Feb 13 11:55:37 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fingerprint.h:13,
+                 from fingerprint.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fingerprint.h:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fraggraph.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fraggraph.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fragment.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from gasteiger.h:8,
+                 from gasteiger.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from gasteiger.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from hungarian.h:7,
+                 from hungarian.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from hungarian.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from library_file.h:9,
+                 from library_file.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from library_file.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from limit_max_change.h:12,
+                 from limit_max_change.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from limit_max_change.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from master_conf.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from master_conf.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from master_score.cpp:2:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from master_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from orient.h:7,
+                 from orient.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from orient.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from sasa.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from sasa.h:14:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_amber.cpp:66:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_amber.cpp:55:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_chemgrid.cpp:39:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_chemgrid.cpp:38:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_descriptor.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_descriptor.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_footprint.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_footprint.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_ph4.h:7,
+                 from score_ph4.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_ph4.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_volume.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_volume.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_gist.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_gist.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_hbond.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_hbond.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_internal.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_internal.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_multigrid.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_multigrid.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_sasa.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_sasa.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_solvent.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_solvent.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from simplex.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from simplex.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from utils.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from utils.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.h:12,
+                 from iso_align.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fragment.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
+                 from rdtyper.cpp:18:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from rdtyper.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from rddrive.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from dockmol.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+cd nab && make all
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
+mv dock6.rdkit ../../bin
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Thu Feb 13 11:58:47 EST 2025.
+(base) [ehspector@dn050 install]$ cd ..
+(base) [ehspector@dn050 alpha_branch]$ exit
+exit
+(base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/test/
+(base) [ehspector@milan1 test]$ ls
+AAQ_noG.mol2  gas_3.in  gas_3.out  gas_3.out_scored.mol2  gas_4.in  test_nocharge.mol2
+(base) [ehspector@milan1 test]$ vi gas_4.in
+(base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 test]$ ls
+AAQ_noG.mol2  gas_3.in  gas_3.out  gas_3.out_scored.mol2  gas_4.in  gas_4.out  test_nocharge.mol2
+(base) [ehspector@milan1 test]$ vi gas_4.out
+(base) [ehspector@milan1 test]$ vi gas_4.in
+(base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 test]$ ls
+AAQ_noG.mol2  gas_3.out              gas_4.in   gas_4.out_scored.mol2
+gas_3.in       gas_3.out_scored.mol2  gas_4.out  test_nocharge.mol2
+(base) [ehspector@milan1 test]$ vi gas_4.out
+(base) [ehspector@milan1 test]$ vi gas_4.in
+(base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan1 test]$ ls
+AAQ_noG.mol2  gas_3.out              gas_4.in   gas_4.out_scored.mol2
+gas_3.in       gas_3.out_scored.mol2  gas_4.out  test_nocharge.mol2
+(base) [ehspector@milan1 test]$ vi gas_4.out
+(base) [ehspector@milan1 test]$ vi gas_4.out_scored.mol2
+(base) [ehspector@milan1 test]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
+short-96c 5een_vs_ ehspecto  R      16:05      3 dg[007-008,041]
+short-96c 2w26_vs_ ehspecto  R    1:27:20      3 dg[032,035-036]
+short-96c 1O86_vs_ ehspecto  R      11:34      3 dg[026,046-047]
+(base) [ehspector@milan1 test]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+(base) [ehspector@milan2 ~]$ scancel 928174
+(base) [ehspector@milan2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan2 ~]$ cd AMS_536/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/007_virtual_screen/
+(base) [ehspector@milan2 007_virtual_screen]$ ls
+virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
+(base) [ehspector@milan2 007_virtual_screen]$ grep -c "Name" virtual_scored.mol2
+(base) [ehspector@milan2 007_virtual_screen]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 5EEN/007_virtualscreen/
+(base) [ehspector@milan2 007_virtualscreen]$ ls
+virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
+(base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2
+(base) [ehspector@milan2 007_virtualscreen]$ cd ../../1O86/007_virtualscreen/
+(base) [ehspector@milan2 007_virtualscreen]$ ls
+virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
+(base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2
+(base) [ehspector@milan2 007_virtualscreen]$ cd ../../
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/
+(base) [ehspector@milan2 006_footprint]$ pwd
+/gpfs/home/ehspector/AMS_536/Tutorials/2w26/006_footprint
+(base) [ehspector@milan2 006_footprint]$ cd ../
+(base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan2 007_virtual_screen]$ ls
+virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
+(base) [ehspector@milan2 007_virtual_screen]$ cd ../../5EEN/
+(base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
+(base) [ehspector@milan2 007_virtualscreen]$ cd ../
+(base) [ehspector@milan2 5EEN]$ cd ../
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ cd 007_virtualscreen/
+(base) [ehspector@milan2 007_virtualscreen]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan2 ~]$ cd AMS_536/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ home
+(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@milan2 dock]$ ls
+amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
+amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
+amber_typer.o       fingerprint.h         nab                   score_internal.o
+base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
+base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
+base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
+base_mpi.cpp        fraggraph.o           orient.h              score.o
+base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
+base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
+base_score.cpp      fragment.o            rddrive.h             score_ph4.o
+base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
+base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
+conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
+conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
+conf_gen_ag.o       grid.h                README                score_solvent.h
+conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
+conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
+conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
+conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
+conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
+conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
+conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
+conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
+conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
+conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
+conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
+conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
+conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
+conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
+conf_gen_hdb.o      lol                   score_footprint.h     trace.o
+defreal.h           Makefile              score_footprint.o     utils.cpp
+dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
+dockmol.cpp         master_conf.h         score_gist.h          utils.o
+dockmol.h           master_conf.o         score_gist.o          version.h
+dockmol.o           master_score.cpp      score.h               xlogp.cpp
+dock.o              master_score.h        score_hbond.cpp       xlogp.h
+filter.cpp          master_score.o        score_hbond.h
+filter.h            mem_info.cpp          score_hbond.o
+(base) [ehspector@milan2 dock]$ ls
+amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
+amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
+amber_typer.o       fingerprint.h         nab                   score_internal.o
+base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
+base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
+base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
+base_mpi.cpp        fraggraph.o           orient.h              score.o
+base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
+base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
+base_score.cpp      fragment.o            rddrive.h             score_ph4.o
+base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
+base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
+conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
+conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
+conf_gen_ag.o       grid.h                README                score_solvent.h
+conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
+conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
+conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
+conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
+conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
+conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
+conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
+conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
+conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
+conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
+conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
+conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
+conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
+conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
+conf_gen_hdb.o      lol                   score_footprint.h     trace.o
+defreal.h           Makefile              score_footprint.o     utils.cpp
+dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
+dockmol.cpp         master_conf.h         score_gist.h          utils.o
+dockmol.h           master_conf.o         score_gist.o          version.h
+dockmol.o           master_score.cpp      score.h               xlogp.cpp
+dock.o              master_score.h        score_hbond.cpp       xlogp.h
+filter.cpp          master_score.o        score_hbond.h
+filter.h            mem_info.cpp          score_hbond.o
+(base) [ehspector@milan2 dock]$ grep parameters
+^C
+(base) [ehspector@milan2 dock]$ grep -c "parameters"
+^C
+(base) [ehspector@milan2 dock]$ grep -c "parameters" library_file.cpp
+(base) [ehspector@milan2 dock]$ vi library_file.cpp
+(base) [ehspector@milan2 dock]$ vi filter.cpp
+(base) [ehspector@milan2 dock]$ vi filter.cpp
+(base) [ehspector@milan2 dock]$ vi dockmol.cpp
+(base) [ehspector@milan2 dock]$ rd
+srun: job 931653 queued and waiting for resources
+srun: job 931653 has been allocated resources
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:28:08 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘mol_status’
+|     if (filter.mol_status = false){
+      |                ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:30:26 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ ls
+alpha_branch  dock6-master  dock6-master.zip  dock6-rdkit
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/
+(base) [ehspector@dn033 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@dn033 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@dn033 src]$ cd dock
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:33:59 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = no){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+dockmol.cpp:917:42: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?
+|     if (filter.gasteigerize.mol_status = no){
+      |                                          ^~
+      |                                          boost::concepts::detail::no
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here
+|   typedef char (&no)[2];
+      |                  ^~
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ ls
+amber_typer.cpp     conf_gen_hdb.o        master_conf.cpp       score.h
+amber_typer.h       defreal.h             master_conf.h         score_hbond.cpp
+amber_typer.o       dock.cpp              master_score.cpp      score_hbond.h
+base_grid.cpp       dockmol.cpp           master_score.h        score_internal.cpp
+base_grid.h         dockmol.h             mem_info.cpp          score_internal.h
+base_grid.o         dock.o                mem_info.h            score_multigrid.cpp
+base_mpi.cpp        filter.cpp            nab                   score_multigrid.h
+base_mpi.h          filter.h              nabcode.h             score_ph4.cpp
+base_mpi.o          fingerprint.cpp       nab.h                 score_ph4.h
+base_score.cpp      fingerprint.h         orient.cpp            score_sasa.cpp
+base_score.h        fraggraph.cpp         orient.h              score_sasa.h
+base_score.o        fraggraph.h           rddrive.cpp           score_solvent.cpp
+conf_gen_ag.cpp     fragment.cpp          rddrive.h             score_solvent.h
+conf_gen_ag.h       fragment.h            rdtyper.cpp           score_volume.cpp
+conf_gen_ag.o       gasteiger.cpp         rdtyper.h             score_volume.h
+conf_gen_cg.cpp     gasteiger.h           README                simplex.cpp
+conf_gen_cg.h       grid.cpp              sasa.cpp              simplex.h
+conf_gen_cg.o       grid.h                sasa.h                sphere.cpp
+conf_gen_dn.cpp     gzstream              score_amber.cpp       sphere.h
+conf_gen_dn_ga.cpp  hungarian.cpp         score_amber.h         tnt
+conf_gen_dn_ga.h    hungarian.h           score_chemgrid.cpp    trace.cpp
+conf_gen_dn_ga.o    iso_align.cpp         score_chemgrid.h      trace.h
+conf_gen_dn.h       iso_align.h           score.cpp             trace.inl
+conf_gen_dn.o       library_file.cpp      score_descriptor.cpp  utils.cpp
+conf_gen_ga.cpp     library_file.h        score_descriptor.h    utils.h
+conf_gen_ga.h       limit_max_change.cpp  score_footprint.cpp   version.h
+conf_gen_ga.o       limit_max_change.h    score_footprint.h     xlogp.cpp
+conf_gen_hdb.cpp    lol                   score_gist.cpp        xlogp.h
+conf_gen_hdb.h      Makefile              score_gist.h
+(base) [ehspector@dn033 dock]$ vi filter.cpp
+(base) [ehspector@dn033 dock]$ vi filter.h
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../
+(base) [ehspector@dn033 alpha_branch]$ ls
+bin        docs     parameters  README.md  template_pipeline
+developer  install  README      src        tutorials
+(base) [ehspector@dn033 alpha_branch]$ cd src/
+(base) [ehspector@dn033 src]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:45:39 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd src/
+(base) [ehspector@dn033 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@dn033 src]$ cd dock
+(base) [ehspector@dn033 dock]$ vi filter.cpp
+(base) [ehspector@dn033 dock]$ cd ../
+(base) [ehspector@dn033 src]$ vi dockmol.cpp
+(base) [ehspector@dn033 src]$ cd dock
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:52:20 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ..
+(base) [ehspector@dn033 alpha_branch]$ cd src/dock
+(base) [ehspector@dn033 dock]$ vi filter.cpp
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ..
+(base) [ehspector@dn033 src]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ ls
+bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
+bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
+config.h   gnu.parallel        ibmaix                   Makefile        test
+configure  gnu.parallel.rdkit  intel                    oneapi
+docker     gnu.rdkit           intel.intelmpi.parallel  pgi
+gnu        gnu.valgrind        intel.ip.mkl             rules.h
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:55:45 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+dockmol.cpp:917:43: warning: multi-character character constant [-Wmultichar]
+|     if (filter.gasteigerize.mol_status == 'no'){
+      |                                           ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status == 'no'){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ..
+(base) [ehspector@dn033 alpha_branch]$ cd src/dock
+(base) [ehspector@dn033 dock]$ vi filter.cpp
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 16:58:13 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ vi library_file.cpp
+(base) [ehspector@dn033 dock]$ vi library_file.h
+(base) [ehspector@dn033 dock]$ vi filter.cpp
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 17:06:34 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:29: error: ‘mol_status’ was not declared in this scope
+|     if (filter.gasteigerize(mol_status) = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+dockmol.cpp:917:39: error: expression cannot be used as a function
+|     if (filter.gasteigerize(mol_status) = false){
+      |                                       ^
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ vi filter.cpp
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ vi filter.cpp
+(base) [ehspector@dn033 dock]$ vi filter.h
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ..
+(base) [ehspector@dn033 src]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 17:16:17 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:917:30: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (!filter.gasteigerize.mol_status){
+      |                              ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd src/dock
+(base) [ehspector@dn033 dock]$ vi library_file.cpp
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 17:59:26 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:780:5: error: ‘mol_status’ was not declared in this scope
+|     mol_status = false;
+      |     ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ vi dockmol.cpp
+(base) [ehspector@dn033 install]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd ../
+(base) [ehspector@dn033 builds]$ cd ../
+(base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ..
+(base) [ehspector@dn033 src]$ cd ../
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 18:02:33 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/
+(base) [ehspector@dn033 src]$ ;s
+bash: syntax error near unexpected token `;'
+(base) [ehspector@dn033 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@dn033 src]$ cd dock
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 18:06:37 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:919:16: error: ‘gasteigerize’ is not a class, namespace, or enumeration
+|     if (filter.gasteigerize::mol_status = no){
+      |                ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
+dockmol.cpp:919:43: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?
+|     if (filter.gasteigerize::mol_status = no){
+      |                                           ^~
+      |                                           boost::concepts::detail::no
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here
+|   typedef char (&no)[2];
+      |                  ^~
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ vi dockmol.cpp
+(base) [ehspector@dn033 install]$ cd ..
+(base) [ehspector@dn033 alpha_branch]$ cd install/
+(base) [ehspector@dn033 install]$ ls
+bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
+bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
+config.h   gnu.parallel        ibmaix                   Makefile        test
+configure  gnu.parallel.rdkit  intel                    oneapi
+docker     gnu.rdkit           intel.intelmpi.parallel  pgi
+gnu        gnu.valgrind        intel.ip.mkl             rules.h
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd ..
+(base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 18:11:54 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:919:16: error: ‘class Filter’ has no member named ‘mol_status’
+|     if (filter.mol_status = false){
+      |                ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ..
+(base) [ehspector@dn033 alpha_branch]$ cd ..
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/
+(base) [ehspector@dn033 src]$ ;s
+bash: syntax error near unexpected token `;'
+(base) [ehspector@dn033 src]$ ls
+accessories  dock       gbsa_grids  Makefile  rdkit  tleap
+antechamber  docktools  grid        mopac6    resp
+(base) [ehspector@dn033 src]$ cd dock
+(base) [ehspector@dn033 dock]$ ls
+amber_typer.cpp     conf_gen_hdb.o        master_conf.cpp       score.h
+amber_typer.h       defreal.h             master_conf.h         score_hbond.cpp
+amber_typer.o       dock.cpp              master_score.cpp      score_hbond.h
+base_grid.cpp       dockmol.cpp           master_score.h        score_internal.cpp
+base_grid.h         dockmol.h             mem_info.cpp          score_internal.h
+base_grid.o         dock.o                mem_info.h            score_multigrid.cpp
+base_mpi.cpp        filter.cpp            nab                   score_multigrid.h
+base_mpi.h          filter.h              nabcode.h             score_ph4.cpp
+base_mpi.o          fingerprint.cpp       nab.h                 score_ph4.h
+base_score.cpp      fingerprint.h         orient.cpp            score_sasa.cpp
+base_score.h        fraggraph.cpp         orient.h              score_sasa.h
+base_score.o        fraggraph.h           rddrive.cpp           score_solvent.cpp
+conf_gen_ag.cpp     fragment.cpp          rddrive.h             score_solvent.h
+conf_gen_ag.h       fragment.h            rdtyper.cpp           score_volume.cpp
+conf_gen_ag.o       gasteiger.cpp         rdtyper.h             score_volume.h
+conf_gen_cg.cpp     gasteiger.h           README                simplex.cpp
+conf_gen_cg.h       grid.cpp              sasa.cpp              simplex.h
+conf_gen_cg.o       grid.h                sasa.h                sphere.cpp
+conf_gen_dn.cpp     gzstream              score_amber.cpp       sphere.h
+conf_gen_dn_ga.cpp  hungarian.cpp         score_amber.h         tnt
+conf_gen_dn_ga.h    hungarian.h           score_chemgrid.cpp    trace.cpp
+conf_gen_dn_ga.o    iso_align.cpp         score_chemgrid.h      trace.h
+conf_gen_dn.h       iso_align.h           score.cpp             trace.inl
+conf_gen_dn.o       library_file.cpp      score_descriptor.cpp  utils.cpp
+conf_gen_ga.cpp     library_file.h        score_descriptor.h    utils.h
+conf_gen_ga.h       limit_max_change.cpp  score_footprint.cpp   version.h
+conf_gen_ga.o       limit_max_change.h    score_footprint.h     xlogp.cpp
+conf_gen_hdb.cpp    lol                   score_gist.cpp        xlogp.h
+conf_gen_hdb.h      Makefile              score_gist.h
+(base) [ehspector@dn033 dock]$ vi dockmol.cpp
+(base) [ehspector@dn033 dock]$ cd ../../install/
+(base) [ehspector@dn033 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Sun Feb 16 18:14:22 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+makIn file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
+dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
+|     if (filter.gasteigerize.mol_status = false){
+      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn033 install]$ cd ../../
+(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn033 dock]$ vi filter.h
+(base) [ehspector@dn033 dock]$ exit
+exit
+(base) [ehspector@milan2 dock]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ home
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock
+(base) [ehspector@milan2 dock]$ vi filter.cpp
+(base) [ehspector@milan2 dock]$ vi filter.cpp
+(base) [ehspector@milan2 dock]$ vi dockmol.cpp
+(base) [ehspector@milan2 dock]$ rd
+srun: job 932106 queued and waiting for resources
+srun: job 932106 has been allocated resources
+(base) [ehspector@dn035 dock]$ cd ../../install/
+(base) [ehspector@dn035 install]$ ls
+bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
+bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
+config.h   gnu.parallel        ibmaix                   Makefile        test
+configure  gnu.parallel.rdkit  intel                    oneapi
+docker     gnu.rdkit           intel.intelmpi.parallel  pgi
+gnu        gnu.valgrind        intel.ip.mkl             rules.h
+(base) [ehspector@dn035 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn035 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 10:08:08 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp:214:7: error: expected unqualified-id before ‘else’
+|     } else {
+      |       ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp:221:5: error: ‘message’ does not name a type
+|     message = get_descriptors(mol);
+      |     ^12:36, 21 February 2025 (EST)~
+filter.cpp:222:5: error: ‘cout’ does not name a type
+|     cout << message << endl;
+      |     ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp:223:1: error: expected declaration before ‘}’ token
+| }
+      | ^
+make[1]: *** [../../install/rules.h:36: filter.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn035 install]$ module load git
+(base) [ehspector@dn035 install]$ git diff
+diff --git a/docs/new_in_6.13.txt b/docs/new_in_6.13.txt
+index 7b10f318..fac269c6 100644
+--- a/docs/new_in_6.13.txt
++++ b/docs/new_in_6.13.txt
+@@ -29,6 +29,14 @@ Ligand Efficiency added for Descriptor Score
+     Users can now toggle ligand efficiency on/off when using grid_score in descriptor score.
+     Ligand efficiency can be used alongside with grid score and will be calculated as the grid score divided by the number of heavy atoms.
++Gasterization of molecules in database filter
++    Users can now apply gasteiger charges using the databasefilter question tree
++    instead of having to gasterize molecules through the GA. This will be a useful
++    tool in benchmarking dock as well as understanding the electrostatics of a
++    protein environment.
++    Disclaimer: gasterization can be used as long as the molecule is precharged
++    and acts mainly as an interconversion function.
++
+ Miscellaneous
+ Mutation Selection algorithmic changes for DOCK_GA
+@@ -36,6 +44,8 @@ Mutation Selection algorithmic changes for DOCK_GA
+     the GA will not select a mutation type and then select a fragment
+     incompatible with the selected mutation type.
++If users use sphere files, DOCK6 will print out the number of spheres used.
++
+:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+ BUG FIXES
+@@ -67,6 +77,8 @@ definitions added:
+  definition    N.am
+  ______________________________________________________________________
++Pertaining to the RDKit compilation with DOCK6, previous versions of DOCK6 included
++a broken Boost url for download. Hence, we have replaced it with a working url.
+:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+@@ -88,6 +100,8 @@ For DOCK_GA:
+     ga_constraint_lower_mol_wt          [0]
+     ga_constraint_lower_mol_wt          [0]
+     ga_constraint_mol_wt_std_dev        [35.0]
++For Database Filter:
++    dbfilter_gasteiger_charges          [no] (yes no)
+:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+@@ -111,6 +125,10 @@ KNOWN BUGS
+. In the flex.defn file, there is a flag minimize which is disabled.
+        (The flag has no impact on the calculation.) All torsions are
+        Minimized.
++
++    4. Gasterization can be used as long as the molecule is precharged
++       and acts mainly as an interconversion function.Additionally,ions
++       will give calculating difficulty.
+:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+diff --git a/src/dock/dockmol.cpp b/src/dock/dockmol.cpp
+index 34811840..2f964a80 100644
+--- a/src/dock/dockmol.cpp
++++ b/src/dock/dockmol.cpp
+@@ -35,7 +35,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #include <iomanip>
+ #include <string.h>
+ #include "dockmol.h"
+-
++#include "filter.h"
+ #ifdef BUILD_DOCK_WITH_RDKIT
+ #include <fstream>
+ // RDKit stuff
+@@ -539,14 +539,14 @@ Read_Mol2_retain(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvat
+             mol.subst_names[i] = subst_name;//mol.title
+         }
+     }
+-    // If all partial charges are zero, it is a bad molecule
++    //If all partial charges are zero, it is a bad molecule
+     int num_zeros = 0;
+     for (int i = 0; i < mol.num_atoms; ++i){
+         if (mol.charges[i] == 0.0){
+             num_zeros += 1;
+         }
+     }
+-    // Is it a bad molecule?
++    //Is it a bad molecule?
+     if (num_zeros == mol.num_atoms){
+         mol.bad_molecule = true;
+     }
+-    // Is it a bad molecule?
++    //Is it a bad molecule?
+     if (num_zeros == mol.num_atoms){
+         mol.bad_molecule = true;
+     } else {
+@@ -775,7 +775,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
+     bool            check_cols = false;
+     bool            seven_columns = false; // default @<TRIPOS>ATOM line has 9 columns. By GDRM
+     //int             bad_line{0}; // number of bad atom lines. By GDRM
+-
++    //declaring classes for gasteiger bypass EHS 2/16/25
++    Filter filter;
++    Filter  mol_status;
+     // init state vars
+     atom_line = false;
+@@ -913,6 +915,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
+         }
+     }
+     // If all partial charges are zero, it is a bad molecule
++    // Skip over if gasterizing a molecule with no charges EHS 2/13/25
++    if (filter.gasteigerize){
++    goto skip;
+     int num_zeros = 0;
+     for (int i = 0; i < mol.num_atoms; ++i){
+         if (mol.charges[i] == 0.0){
+@@ -925,6 +930,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
+     } else {
+         mol.bad_molecule = false;
+     }
++}
++    skip:
++       cout << "This Molecule has no charges and will be gasterized" << endl;
+     // skip down to the bond section
+     for (;;) {
+diff --git a/src/dock/filter.cpp b/src/dock/filter.cpp
+index b8469418..58f9c742 100644
+--- a/src/dock/filter.cpp
++++ b/src/dock/filter.cpp
+@@ -196,14 +196,14 @@ void Filter::calc_descriptors(DOCKMol & mol, AMBER_TYPER & c_typer)
+         }
+         // placing a gasteiger flag this will be similar to ga code
+-        if ( gasteigerize ){
+-            //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25
+-            activate_mol(mol);
++        if ( gasteigerize && mol.bad_molecule == false ){
++            //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25
++           activate_mol(mol);
+(base) [ehspector@dn035 install]$
+(base) [ehspector@dn035 install]$ exit
+exit
+(base) [ehspector@milan2 dock]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ home
+(base) [ehspector@milan2 espector]$ cd 4s0v/
+(base) [ehspector@milan2 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@milan2 4s0v]$ cd gas_teiger/
+(base) [ehspector@milan2 gas_teiger]$ ls
+AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out_scored.mol2  no_gas.in
+gas_2.in               gas_4.out              gas.in                 no_gas.out
+gas_2.out              gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
+gas_2.out_scored.mol2  gas_5.in               gas.out_scored.mol2    test
+gas_3.out              gas_5.out              no_charge              test.mol2
+(base) [ehspector@milan2 gas_teiger]$ cd test/
+(base) [ehspector@milan2 test]$ ls
+AAQ_noG.mol2  gas_3.out              gas_4.in   gas_4.out_scored.mol2
+gas_3.in       gas_3.out_scored.mol2  gas_4.out  test_nocharge.mol2
+(base) [ehspector@milan2 test]$ vi gas_4.out
+(base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2
+(base) [ehspector@milan2 test]$ dock6 -i gas_4.in -o gas_4.out
+(base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2
+(base) [ehspector@milan2 test]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ home
+(base) [ehspector@milan1 espector]$ cd 4s0v/
+(base) [ehspector@milan1 4s0v]$ ls
+cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
+Denovodata              flex_docking          fragLib     gridbox        virtual_screening
+deNovorefinement        flex_docking_mpi      GA          reScore
+dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
+energy_min              focusReScore          gas_teiger  structure
+(base) [ehspector@milan1 4s0v]$ cd ../builds/alpha_branch/src/
+(base) [ehspector@milan1 src]$ cd dock
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ vi dock.cpp
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ grep -wc Read_Mol2 *
+amber_typer.cpp:0
+amber_typer.h:0
+amber_typer.o:0
+base_grid.cpp:0
+base_grid.h:0
+base_grid.o:0
+base_mpi.cpp:0
+base_mpi.h:0
+base_mpi.o:0
+base_score.cpp:0
+base_score.h:0
+base_score.o:0
+conf_gen_ag.cpp:0
+conf_gen_ag.h:0
+conf_gen_ag.o:0
+conf_gen_cg.cpp:0
+conf_gen_cg.h:0
+conf_gen_cg.o:0
+conf_gen_dn.cpp:2
+conf_gen_dn_ga.cpp:1
+conf_gen_dn_ga.h:0
+conf_gen_dn_ga.o:0
+conf_gen_dn.h:0
+conf_gen_dn.o:0
+conf_gen_ga.cpp:1
+conf_gen_ga.h:0
+conf_gen_ga.o:0
+conf_gen_hdb.cpp:0
+conf_gen_hdb.h:0
+conf_gen_hdb.o:0
+defreal.h:0
+dock.cpp:0
+dockmol.cpp:1
+dockmol.h:1
+dockmol.o:0
+dock.o:0
+filter.cpp:0
+filter.h:0
+fingerprint.cpp:1
+fingerprint.h:0
+fraggraph.cpp:0
+fraggraph.h:0
+fragment.cpp:0
+fragment.h:0
+gasteiger.cpp:0
+gasteiger.h:0
+grid.cpp:0
+grid.h:0
+grep: gzstream: Is a directory
+gzstream:0
+hungarian.cpp:0
+hungarian.h:0
+iso_align.cpp:0
+iso_align.h:0
+library_file.cpp:2
+library_file.h:0
+limit_max_change.cpp:0
+limit_max_change.h:0
+lol:0
+Makefile:0
+master_conf.cpp:0
+master_conf.h:0
+master_score.cpp:0
+master_score.h:0
+mem_info.cpp:0
+mem_info.h:0
+grep: nab: Is a directory
+nab:0
+nabcode.h:0
+nab.h:0
+orient.cpp:0
+orient.h:0
+rddrive.cpp:0
+rddrive.h:0
+rdtyper.cpp:0
+rdtyper.h:0
+README:0
+sasa.cpp:0
+sasa.h:0
+score_amber.cpp:0
+score_amber.h:0
+score_chemgrid.cpp:0
+score_chemgrid.h:0
+score.cpp:1
+score_descriptor.cpp:2
+score_descriptor.h:0
+score_footprint.cpp:2
+score_footprint.h:0
+score_gist.cpp:0
+score_gist.h:0
+score.h:0
+score_hbond.cpp:1
+score_hbond.h:0
+score_internal.cpp:0
+score_internal.h:0
+score_multigrid.cpp:1
+score_multigrid.h:0
+score_ph4.cpp:2
+score_ph4.h:0
+score_sasa.cpp:1
+score_sasa.h:0
+score_solvent.cpp:1
+score_solvent.h:0
+score_volume.cpp:1
+score_volume.h:0
+simplex.cpp:0
+simplex.h:0
+sphere.cpp:0
+sphere.h:0
+grep: tnt: Is a directory
+tnt:0
+trace.cpp:0
+trace.h:0
+trace.inl:0
+utils.cpp:0
+utils.h:0
+version.h:0
+xlogp.cpp:0
+xlogp.h:0
+(base) [ehspector@milan1 dock]$ vi library_file.cpp
+(base) [ehspector@milan1 dock]$ vi dock.cpp
+(base) [ehspector@milan1 dock]$ vi dock.cpp
+(base) [ehspector@milan1 dock]$ vi dock.cpp
+(base) [ehspector@milan1 dock]$ vi library_file.cpp
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ vi dock.cpp
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi dock.cpp
+(base) [ehspector@milan1 dock]$ vi library_file.cpp
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi filter.h
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi filter.h
+(base) [ehspector@milan1 dock]$ vi filter.cpp
+(base) [ehspector@milan1 dock]$ vi dockmol.cpp
+(base) [ehspector@milan1 dock]$ rd
+srun: job 932383 queued and waiting for resources
+srun: job 932383 has been allocated resources
+(base) [ehspector@dn051 dock]$ cd ../../install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 12:54:43 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp:214:7: error: expected unqualified-id before ‘else’
+|     } else {
+      |       ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp:221:5: error: ‘message’ does not name a type
+|     message = get_descriptors(mol);
+      |     ^12:36, 21 February 2025 (EST)~
+filter.cpp:222:5: error: ‘cout’ does not name a type
+|     cout << message << endl;
+      |     ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp:223:1: error: expected declaration before ‘}’ token
+| }
+      | ^
+make[1]: *** [../../install/rules.h:36: filter.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn051 install]$ cd ../../
+(base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn051 dock]$ vi filter.cpp
+(base) [ehspector@dn051 dock]$ cd ../../install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 13:00:19 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+filter.cpp: In member function ‘void Filter::calc_descriptors(DOCKMol&, AMBER_TYPER&)’:
+filter.cpp:279:26: error: qualified-id in declaration before ‘(’ token
+| bool Filter::fails_filter(DOCKMol & mol)
+      |                          ^
+filter.cpp:529:31: error: qualified-id in declaration before ‘(’ token
+| string Filter::get_descriptors(DOCKMol & mol)
+      |                               ^
+filter.cpp:591:21: error: qualified-id in declaration before ‘(’ token
+| Filter::activate_mol( DOCKMol & mol )
+      |                     ^
+filter.cpp:605:2: error: expected ‘}’ at end of input
+| } // end Filter::activate_mol()
+      |  ^
+filter.cpp:147:1: note: to match this ‘{’
+| {
+      | ^
+make[1]: *** [../../install/rules.h:36: filter.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn051 install]$ cd ../../alpha_branch/src/dock
+(base) [ehspector@dn051 dock]$ vi filter.cpp
+(base) [ehspector@dn051 dock]$ vi filter.cpp
+(base) [ehspector@dn051 dock]$ cd ../../install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 13:05:08 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fingerprint.h:13,
+                 from fingerprint.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fingerprint.h:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fraggraph.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fraggraph.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fragment.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from gasteiger.h:8,
+                 from gasteiger.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from gasteiger.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from hungarian.h:7,
+                 from hungarian.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from hungarian.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from library_file.h:9,
+                 from library_file.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from library_file.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from limit_max_change.h:12,
+                 from limit_max_change.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from limit_max_change.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from master_conf.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from master_conf.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from master_score.cpp:2:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from master_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from orient.h:7,
+                 from orient.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from orient.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from sasa.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from sasa.h:14:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_amber.cpp:66:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_amber.cpp:55:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_chemgrid.cpp:39:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_chemgrid.cpp:38:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_descriptor.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_descriptor.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_footprint.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_footprint.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_ph4.h:7,
+                 from score_ph4.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_ph4.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_volume.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_volume.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_gist.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_gist.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_hbond.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_hbond.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_internal.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_internal.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_multigrid.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_multigrid.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_sasa.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_sasa.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_solvent.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_solvent.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from simplex.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from simplex.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from utils.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from utils.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.h:12,
+                 from iso_align.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fragment.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
+                 from rdtyper.cpp:18:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from rdtyper.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from rddrive.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from dockmol.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+cd nab && make all
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
+mv dock6.rdkit ../../bin
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+Installation of
+DOCK v6.12
+program dock is complete at Mon Feb 17 13:08:09 EST 2025.
+(base) [ehspector@dn051 install]$ cd ../al
+bash: cd: ../al: No such file or directory
+(base) [ehspector@dn051 install]$ cd ../../alpha_branch/
+(base) [ehspector@dn051 alpha_branch]$ cd src/dock
+(base) [ehspector@dn051 dock]$ vi filter.cpp
+(base) [ehspector@dn051 dock]$ vi filter.cpp
+(base) [ehspector@dn051 dock]$ vi dock.cpp
+(base) [ehspector@dn051 dock]$ vi library_file.cpp
+(base) [ehspector@dn051 dock]$ vi dockmol.cpp
+(base) [ehspector@dn051 dock]$ vi dockmol.cpp
+(base) [ehspector@dn051 dock]$ cd ../../
+(base) [ehspector@dn051 alpha_branch]$ cd install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 13:31:34 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dock.cpp: In function ‘int main(int, char**)’:
+dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
+|     while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
+      |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+In file included from dock.cpp:62:
+library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
+|     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
+      |                     ^12:36, 21 February 2025 (EST)~
+library_file.h:141:21: note:   candidate expects 7 arguments, 8 provided
+make[1]: *** [../../install/rules.h:36: dock.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn051 install]$ cd ../
+(base) [ehspector@dn051 alpha_branch]$ cd ../
+(base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn051 dock]$ vi dock.cpp
+(base) [ehspector@dn051 dock]$ vi library_file.cpp
+(base) [ehspector@dn051 dock]$ vi dockmol.cpp
+(base) [ehspector@dn051 dock]$ ls
+amber_typer.cpp     conf_gen_dn.o     gzstream              rddrive.h             score_multigrid.h
+amber_typer.h       conf_gen_ga.cpp   hungarian.cpp         rdtyper.cpp           score_ph4.cpp
+amber_typer.o       conf_gen_ga.h     hungarian.h           rdtyper.h             score_ph4.h
+base_grid.cpp       conf_gen_ga.o     iso_align.cpp         README                score_sasa.cpp
+base_grid.h         conf_gen_hdb.cpp  iso_align.h           sasa.cpp              score_sasa.h
+base_grid.o         conf_gen_hdb.h    library_file.cpp      sasa.h                score_solvent.cpp
+base_mpi.cpp        conf_gen_hdb.o    library_file.h        score_amber.cpp       score_solvent.h
+base_mpi.h          defreal.h         limit_max_change.cpp  score_amber.h         score_volume.cpp
+base_mpi.o          dock.cpp          limit_max_change.h    score_chemgrid.cpp    score_volume.h
+base_score.cpp      dockmol.cpp       lol                   score_chemgrid.h      simplex.cpp
+base_score.h        dockmol.h         Makefile              score.cpp             simplex.h
+base_score.o        filter.cpp        master_conf.cpp       score_descriptor.cpp  sphere.cpp
+conf_gen_ag.cpp     filter.h          master_conf.h         score_descriptor.h    sphere.h
+conf_gen_ag.h       fingerprint.cpp   master_score.cpp      score_footprint.cpp   tnt
+conf_gen_ag.o       fingerprint.h     master_score.h        score_footprint.h     trace.cpp
+conf_gen_cg.cpp     fraggraph.cpp     mem_info.cpp          score_gist.cpp        trace.h
+conf_gen_cg.h       fraggraph.h       mem_info.h            score_gist.h          trace.inl
+conf_gen_cg.o       fragment.cpp      nab                   score.h               utils.cpp
+conf_gen_dn.cpp     fragment.h        nabcode.h             score_hbond.cpp       utils.h
+conf_gen_dn_ga.cpp  gasteiger.cpp     nab.h                 score_hbond.h         version.h
+conf_gen_dn_ga.h    gasteiger.h       orient.cpp            score_internal.cpp    xlogp.cpp
+conf_gen_dn_ga.o    grid.cpp          orient.h              score_internal.h      xlogp.h
+conf_gen_dn.h       grid.h            rddrive.cpp           score_multigrid.cpp
+(base) [ehspector@dn051 dock]$ vi dockmol.cpp
+(base) [ehspector@dn051 dock]$ vi dock.cpp
+(base) [ehspector@dn051 dock]$ vi library_file.cpp
+(base) [ehspector@dn051 dock]$ vi dock.cpp
+(base) [ehspector@dn051 dock]$ cd ../../
+(base) [ehspector@dn051 alpha_branch]$ cd install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 13:40:15 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+dock.cpp: In function ‘int main(int, char**)’:
+dock.cpp:340:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool, bool, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
+|     while (c_library.get_mol(mol, false, false, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
+      |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)
+In file included from dock.cpp:62:
+library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
+|     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
+      |                     ^12:36, 21 February 2025 (EST)~
+library_file.h:141:21: note:   candidate expects 7 arguments, 8 provided
+dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
+|     while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
+      |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
+library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
+|     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
+      |                     ^12:36, 21 February 2025 (EST)~
+library_file.h:141:21: note:   candidate expects 7 arguments, 8 provided
+make[1]: *** [../../install/rules.h:36: dock.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn051 install]$ cd ..
+(base) [ehspector@dn051 alpha_branch]$ cd ..
+(base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
+(base) [ehspector@dn051 dock]$ vi library_file.h
+(base) [ehspector@dn051 dock]$ cd ../../install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 13:45:32 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fingerprint.h:13,
+                 from fingerprint.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fingerprint.h:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fraggraph.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fraggraph.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fragment.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from gasteiger.h:8,
+                 from gasteiger.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from gasteiger.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from hungarian.h:7,
+                 from hungarian.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from hungarian.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from library_file.h:9,
+                 from library_file.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from library_file.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+library_file.cpp: In member function ‘void Library_File::open_files()’:
+library_file.cpp:1384:21: error: no matching function for call to ‘Library_File::read_mol(DOCKMol&, bool’
+|         if (read_mol(tmp_mol, false))
+      |             12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)
+library_file.h:139:21: note: candidate: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’
+|     bool            read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
+      |                     ^12:36, 21 February 2025 (EST)~~
+library_file.h:139:21: note:   candidate expects 3 arguments, 2 provided
+library_file.cpp: At global scope:
+library_file.cpp:1435:1: error: no declaration matches ‘bool Library_File::read_mol(DOCKMol&, bool)’
+| Library_File::read_mol(DOCKMol & mol, bool read_amber)
+      | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
+library_file.h:139:21: note: candidate is: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’
+|     bool            read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
+      |                     ^12:36, 21 February 2025 (EST)~~
+library_file.h:19:17: note: ‘class Library_File’ defined here
+| class           Library_File:public Base_MPI {
+      |                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
+make[1]: *** [../../install/rules.h:36: library_file.o] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn051 install]$ cd ..
+(base) [ehspector@dn051 alpha_branch]$ cd src/dock
+(base) [ehspector@dn051 dock]$ vi dock.cpp
+(base) [ehspector@dn051 dock]$ vi library_file.cpp
+(base) [ehspector@dn051 dock]$ cd ../../install/
+(base) [ehspector@dn051 install]$ make clean
+make -C ../src  clean
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+make -C dock  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
+cd nab && make clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+/bin/rm -f *.o nab.a lex.mm_options.c
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make cleanall
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make -C accessories  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+/bin/rm -f showbox.o showsphere.o sphgen.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
+make -C gbsa_grids  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C schemgrid_GB  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
+make -C schemgrid_SA  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
+make -C grid  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
+make -C tleap  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
+make -C antechamber  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+/bin/rm -f *.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
+make -C mopac6/src  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
+make -C resp  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+/bin/rm -f amopen.o lapack.o mexit.o resp.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
+make -C docktools  clean
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make -C chemgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
+make -C solvgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
+make -C solvgrids_sev  clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+/bin/rm -f sas.o cube.o memalloc.o solvmap.o
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
+make -C convgrids      clean
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridconv.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make -f gridrdsl.mk clean
+make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
+make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
+(base) [ehspector@dn051 install]$ make dock
+Starting installation of
+DOCK v6.12
+program dock at Mon Feb 17 13:53:32 EST 2025.
+make -C ../src/dock  install
+make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from amber_typer.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from amber_typer.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_mpi.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
+                 from base_mpi.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from base_score.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from base_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ag.h:5,
+                 from conf_gen_ag.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ag.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_cg.h:5,
+                 from conf_gen_cg.cpp:17:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_cg.cpp:8:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn.h:12,
+                 from conf_gen_dn.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_dn_ga.h:12,
+                 from conf_gen_dn_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_dn_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_ga.h:13,
+                 from conf_gen_ga.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from conf_gen_ga.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from conf_gen_hdb.h:4,
+                 from conf_gen_hdb.cpp:14:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from conf_gen_hdb.cpp:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from dock.cpp:61:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dock.cpp:53:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from dockmol.cpp:37:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from dockmol.cpp:33:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from filter.h:10,
+                 from filter.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from filter.h:4:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fingerprint.h:13,
+                 from fingerprint.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fingerprint.h:6:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fraggraph.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fraggraph.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.cpp:3:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from fragment.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from gasteiger.h:8,
+                 from gasteiger.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from gasteiger.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from hungarian.h:7,
+                 from hungarian.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from hungarian.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from library_file.h:9,
+                 from library_file.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from library_file.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from limit_max_change.h:12,
+                 from limit_max_change.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from limit_max_change.h:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from master_conf.h:6,
+                 from master_conf.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from master_conf.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from master_score.cpp:2:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from master_score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from orient.h:7,
+                 from orient.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from orient.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from sasa.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from sasa.h:14:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_amber.cpp:66:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_amber.cpp:55:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_chemgrid.cpp:39:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
+                 from score_chemgrid.cpp:38:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_descriptor.cpp:10:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_descriptor.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_footprint.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_footprint.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_ph4.h:7,
+                 from score_ph4.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_ph4.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_volume.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_volume.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_gist.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_gist.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_hbond.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_hbond.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_internal.cpp:8:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_internal.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score_multigrid.cpp:9:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_multigrid.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_sasa.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_sasa.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from score_solvent.h:9,
+                 from sasa.h:15,
+                 from score_solvent.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from score_solvent.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from score.h:7,
+                 from master_score.h:5,
+                 from simplex.cpp:4:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from simplex.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from utils.cpp:7:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from utils.cpp:1:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from fragment.h:12,
+                 from iso_align.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
+                 from fragment.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
+                 from rdtyper.cpp:18:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
+                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
+                 from rdtyper.cpp:2:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
+In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
+                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
+                 from dockmol.h:16,
+                 from rddrive.cpp:1:
+/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
+|         struct hash_base : std::unary_function<T, std::size_t> {};
+      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
+                 from dockmol.h:5:
+/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
+|     struct unary_function
+      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
+cd nab && make all
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+gcc -c -O3 -D_ANSI_SOURCE  molio.c
+gcc -c  -O2 -o prm.o  prm.c
+make is_LEX_available
+make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
+gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
+gcc -c  -O2 -o traceback.o  traceback.c
+gcc -c  -O2 -o select_atoms.o  select_atoms.c
+gcc -c  -O2 -o memutil.o  memutil.c
+gcc -c  -O2 -o reslib.o  reslib.c
+gcc -c  -O2 -o jacobi.o  jacobi.c
+gcc -c  -O2 -o molutil.o  molutil.c
+gcc -c  -O2 -o chirvol.o  chirvol.c
+gcc -c  -O2 -o regexp.o  regexp.c
+gcc -c  -O2 -o binpos.o  binpos.c
+gcc -c  -O2 -o time.o  time.c
+gcc -c -O3 -D_ANSI_SOURCE  rand2.c
+gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
+gcc -c  -O2 -o database.o  database.c
+gcc -c  -O2 -o tleap.o  tleap.c
+ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
+ar: creating nab.a
+a - molio.o
+a - prm.o
+a - sff.o
+a - traceback.o
+a - select_atoms.o
+a - memutil.o
+a - reslib.o
+a - jacobi.o
+a - molutil.o
+a - chirvol.o
+a - regexp.o
+a - binpos.o
+a - time.o
+a - rand2.o
+a - conjgrad.o
+a - database.o
+a - tleap.o
+ranlib nab.a
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
+cd gzstream && make
+make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
+ar cr libgzstream.a gzstream.o
+make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
+g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
+	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
+conf_gen_dn.o: In function `DN_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
+conf_gen_dn.cpp:(.text+0x1ec40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
+conf_gen_dn.o: In function `DN_Build::read_library_anchor(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
+conf_gen_dn.cpp:(.text+0x1f508): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
+conf_gen_dn_ga.o: In function `DN_GA_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
+conf_gen_dn_ga.cpp:(.text+0xdf40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
+conf_gen_ga.o: In function `GA_Recomb::read_library(std::vector<DOCKMol, std::allocator<DOCKMol> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
+conf_gen_ga.cpp:(.text+0x1d5c5): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
+fingerprint.o: In function `Fingerprint::input_parameters(Parameter_Reader&)':
+fingerprint.cpp:(.text+0x2f14): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
+library_file.o:library_file.cpp:(.text+0x6c75): more undefined references to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' follow
+collect2: error: ld returned 1 exit status
+make[1]: *** [Makefile:39: dock6.rdkit] Error 1
+make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+make: *** [Makefile:28: dock] Error 2
+(base) [ehspector@dn051 install]$ exiy
+bash: exiy: command not found
+(base) [ehspector@dn051 install]$ exit
+exit
+srun: error: dn051: task 0: Exited with exit code 127
+(base) [ehspector@milan1 dock]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ mkdir test
+(base) [ehspector@milan1 AMS_536]$ mkdir test
+mkdir: cannot create directory ‘test’: File exists
+(base) [ehspector@milan1 AMS_536]$ mkdir move
+(base) [ehspector@milan1 AMS_536]$ mv test/ move/
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  move  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ rm -r move
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd class_project/
+(base) [ehspector@milan1 class_project]$ ls
+(base) [ehspector@milan1 class_project]$ cd T
+-bash: cd: T: No such file or directory
+(base) [ehspector@milan1 class_project]$ ls
+(base) [ehspector@milan1 class_project]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
+_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
+_gridbox          006_footprint  009_rescore         Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan1 Robs_new_2w26]$ ls
+_test       002_spheres  004_dock      006_ga_lib
+_structure  003_grid     005_analysis  007_ga_run1
+(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan1 2w26]$ mkdir ga_calc
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_new_2w26
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               test4.tar
+_gridbox          006_footprint  009_rescore         Robs_2w26
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ vi N
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
+(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan1 Robs_new_2w26]$ ls
+_test       002_spheres  004_dock      006_ga_lib
+_structure  003_grid     005_analysis  007_ga_run1
+(base) [ehspector@milan1 Robs_new_2w26]$ cd 006_ga_lib/
+(base) [ehspector@milan1 006_ga_lib]$ ls
+lib.sh                  2W26.fraglib.out             2W26_fragout_scored.mol2
+combine.sh              2W26_fraglib_rigid.mol2      full_fraglib.dat
+W26.fraglib.in           2W26_fraglib_scaffold.mol2   full_sorted_fraglib.dat
+W26_fraglib_linker.mol2  2W26_fraglib_sidechain.mol2  unique_full_sorted_fraglib.dat
+W26.fraglib.log          2W26_fraglib_torenv.dat
+(base) [ehspector@milan1 006_ga_lib]$ vi 2W26.fraglib.in
+(base) [ehspector@milan1 006_ga_lib]$ cd ..
+(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/006_ga_lib/2W26.fraglib.in ga_calc/2w26_fraglib.in
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_new_2w26
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               test4.tar
+_gridbox          006_footprint  009_rescore         Robs_2w26
+(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
+(base) [ehspector@milan1 007_virtual_screen]$ ls
+virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
+(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
+(base) [ehspector@milan1 007_virtual_screen]$ cd ..
+(base) [ehspector@milan1 2w26]$ cp 004_energymin/min.sh ga_calc/lib.sh
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_new_2w26
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               test4.tar
+_gridbox          006_footprint  009_rescore         Robs_2w26
+(base) [ehspector@milan1 2w26]$ cd ga_calc/
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in  lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
+(base) [ehspector@milan1 ga_calc]$ cd ../001_structure/
+(base) [ehspector@milan1 001_structure]$ ls
+w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
+w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
+(base) [ehspector@milan1 001_structure]$ cd ../ga_calc/
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in  lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
+(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
+(base) [ehspector@milan1 ga_calc]$ bash lib.sh
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in           2W26_fraglib_rigid.mol2     2W26_fraglib_sidechain.mol2
+W26_fraglib_linker.mol2  2W26_fraglib_scaffold.mol2  2W26_fraglib_torenv.dat
+w26_fraglib.out          2w26_fraglib_scored.mol2    lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.out
+(base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_scaffold.mol2
+(base) [ehspector@milan1 ga_calc]$ grep -c "lnk" 2W26_fraglib_linker.mol2
+(base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_linker.mol2
+(base) [ehspector@milan1 ga_calc]$ vi py.sh
+(base) [ehspector@milan1 ga_calc]$ vi lib.sh.sh
+(base) [ehspector@milan1 ga_calc]$ vi lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi py.sh
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in           2W26_fraglib_rigid.mol2     2W26_fraglib_sidechain.mol2  py.sh
+W26_fraglib_linker.mol2  2W26_fraglib_scaffold.mol2  2W26_fraglib_torenv.dat
+w26_fraglib.out          2w26_fraglib_scored.mol2    lib.sh
+(base) [ehspector@milan1 ga_calc]$ vi py.sh
+(base) [ehspector@milan1 ga_calc]$ module load python
+(base) [ehspector@milan1 ga_calc]$ bash py.sh
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
+W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
+w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
+W26_fraglib_rigid.mol2     full_fraglib.dat
+W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
+(base) [ehspector@milan1 ga_calc]$ cd ..
+(base) [ehspector@milan1 2w26]$ mkdir ga_run
+(base) [ehspector@milan1 2w26]$ cd ga_run/
+(base) [ehspector@milan1 ga_run]$ ls
+(base) [ehspector@milan1 ga_run]$ touch 2w26_ga.in
+(base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic
+Genetic Algorithm Recombination Parameters
+------------------------------------------------------------------------------------------
+                                             ga_molecule_file [ga_molecule_file.mol2] ():../001_structure/2w26_ligand_H_cH.mol2
+                                                 ga_utilities [no] (yes no):
+                                     ga_fraglib_scaffold_file [fraglib_scaffold.mol2] ():
+                                       ga_fraglib_linker_file [fraglib_linker.mol2] ():
+                                    ga_fraglib_sidechain_file [fraglib_sidechain.mol2] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
+                                              ga_torenv_table [fraglib_torenv.dat] ():../ga_calc/unique_full_sorted_fraglib.dat
+                                           ga_max_generations [100] ():5
+                                                  ga_xover_on [yes] (yes no):
+                                ga_xover_sampling_method_rand [yes] (yes no):
+                                                 ga_xover_max [150] ():
+                                            ga_bond_tolerance [0.5] ():
+                                              ga_angle_cutoff [0.14] ():
+                                             ga_check_overlap [no] (yes no):
+                                           ga_mutate_addition [yes] (yes no):
+                                           ga_mutate_deletion [yes] (yes no):
+                                       ga_mutate_substitution [yes] (yes no):
+                                        ga_mutate_replacement [yes] (yes no):
+                                            ga_mutate_parents [no] (yes no):yes
+                                                 ga_pmut_rate [0.3] ():
+                                                 ga_omut_rate [0.7] ():
+                                            ga_max_mut_cycles [5] ():
+                                       ga_mut_sampling_method [rand] (rand | graph):
+                                          ga_num_random_picks [15] ():
+                                             ga_max_root_size [5] ():
+                                             ga_energy_cutoff [100] ():
+                                        ga_heur_unmatched_num [1] ():
+                                         ga_heur_matched_rmsd [0.5] ():
+                                         ga_constraint_mol_wt [500] ():
+                                        ga_constraint_rot_bon [10] ():
+                                       ga_constraint_H_accept [10] ():
+                                          ga_constraint_H_don [5] ():
+                                  ga_constraint_formal_charge [2] ():
+                                             ga_ensemble_size [200] ():100
+                                          ga_selection_method [elitism] (elitism | tournament | roulette):
+                                          ga_elitism_combined [yes] (yes no):
+                                            ga_elitism_option [max] (percent | number | max):
+                             ga_max_num_gen_with_no_crossover [25] ():
+                                           ga_name_identifier [ga] ():
+                                             ga_output_prefix [ga_output] ():2w26_ga
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):no
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+                                           gist_score_primary [no] (yes no):
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+                                      multigrid_score_primary [no] (yes no):
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+                                        dock3.5_score_primary [no] (yes no):
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+                                     continuous_score_primary [no] (yes no):
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+                           footprint_similarity_score_primary [no] (yes no):
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+                                  pharmacophore_score_primary [no] (yes no):
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+                                          hbond_score_primary [no] (yes no):
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+                                internal_energy_score_primary [no] (yes no):
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+                                     descriptor_score_primary [no] (yes no):
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+                                       gbsa_zou_score_primary [no] (yes no):
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+                                   gbsa_hawkins_score_primary [no] (yes no):
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+                                           SASA_score_primary [no] (yes no):
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+                                          amber_score_primary [no] (yes no):
+Error:  No scoring function selected for the primary score.  Program will now terminate.
+(base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in
+(base) [ehspector@milan1 ga_run]$ ls
+w26_ga.in
+(base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in
+(base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic
+Genetic Algorithm Recombination Parameters
+------------------------------------------------------------------------------------------
+                                             ga_molecule_file [ga_molecule_file.mol2] ():^C
+(base) [ehspector@milan1 ga_run]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_2w26
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_new_2w26
+_gridbox          006_footprint  009_rescore         ga_run                test4.tar
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ bash commands.txt
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  protein  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd protein/
+(base) [ehspector@milan1 protein]$ ls
+_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min
+(base) [ehspector@milan1 protein]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ rm -r protein/
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_2w26
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_new_2w26
+_gridbox          006_footprint  009_rescore         ga_run                test4.tar
+(base) [ehspector@milan1 2w26]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan2 ~]$ cd AMS_536/
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run/
+(base) [ehspector@milan2 ga_run]$ ls
+w26_ga.in  2w26_ga_lib.in
+(base) [ehspector@milan2 ga_run]$ vi 2w26_ga_lib.in
+(base) [ehspector@milan2 ga_run]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd Robs_new_2w26/
+(base) [ehspector@milan2 Robs_new_2w26]$ cd 007_ga_run1/
+(base) [ehspector@milan2 007_ga_run1]$ ls
+W26_ga.in   2W26_ga.restart0000.mol2  2W26_ga.restart0002.mol2  2W26_ga.restart0004.mol2
+W26_ga.out  2W26_ga.restart0001.mol2  2W26_ga.restart0003.mol2  2W26_ga.restart0005.mol2
+(base) [ehspector@milan2 007_ga_run1]$ vi 2W26_ga.in
+(base) [ehspector@milan2 007_ga_run1]$ cd ..
+(base) [ehspector@milan2 Robs_new_2w26]$ ls
+_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
+(base) [ehspector@milan2 Robs_new_2w26]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ga_run/
+(base) [ehspector@milan2 ga_run]$ ls
+w26_ga.in  2w26_ga_lib.in
+(base) [ehspector@milan2 ga_run]$ rm 2w26_ga_lib.in
+(base) [ehspector@milan2 ga_run]$ vi 2w26_ga.in
+(base) [ehspector@milan2 ga_run]$ rm 2w26_ga.in
+(base) [ehspector@milan2 ga_run]$ cd ..
+(base) [ehspector@milan2 2w26]$ cp Robs_new_2w26/007_ga_run1/2W26_ga.in ga_calc/2w26_ga.in
+(base) [ehspector@milan2 2w26]$ mv ga_calc/2w26_ga.in ga_run/
+(base) [ehspector@milan2 2w26]$ mv ga_run/ ga_run_5
+(base) [ehspector@milan2 2w26]$ mkdir ga_run_50
+(base) [ehspector@milan2 2w26]$ cd ga_run_5
+(base) [ehspector@milan2 ga_run_5]$ ls
+w26_ga.in
+(base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in
+(base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out
+(base) [ehspector@milan2 ga_run_5]$ ls
+w26_ga.in  2w26_ga.out
+(base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.out
+(base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in
+(base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out
+(base) [ehspector@milan2 ga_run_5]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0002.mol2  2w26_5_ga.restart0004.mol2  2w26_ga.in
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0005.mol2  2w26_ga.out
+(base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.in 2w26_ga_5.in
+(base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.out 2w26_ga_5.out
+(base) [ehspector@milan2 ga_run_5]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0002.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_5.in
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0005.mol2  2w26_ga_5.out
+(base) [ehspector@milan2 ga_run_5]$ cd ..
+(base) [ehspector@milan2 2w26]$ cp ga_run_5/2w26_ga_5.in ga_run_50/2w26_ga_50.in
+(base) [ehspector@milan2 2w26]$ cp 007_virtual_screen/virtual.sh ga_run_50/ga.sh
+(base) [ehspector@milan2 2w26]$ cd ga_run_50
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_ga_50.in  ga.sh
+(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
+(base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
+(base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
+(base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
+(base) [ehspector@milan2 ga_run_50]$ avail
+PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
+a100                      up    8:00:00      2   mix@ a100-[02,04]
+a100                      up    8:00:00      8 alloc@ a100-[03,05-11]
+a100                      up    8:00:00      1 drain* a100-01
+a100-large                up    8:00:00      2   mix@ a100-[02,04]
+a100-large                up    8:00:00      8 alloc@ a100-[03,05-11]
+a100-large                up    8:00:00      1 drain* a100-01
+a100-long                 up 2-00:00:00      2   mix@ a100-[02,04]
+a100-long                 up 2-00:00:00      8 alloc@ a100-[03,05-11]
+a100-long                 up 2-00:00:00      1 drain* a100-01
+debug-40core              up    1:00:00      2 drain* dn[031,037]
+debug-40core              up    1:00:00      1  drain dn061
+debug-40core              up    1:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+debug-40core              up    1:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+extended-40core           up 7-00:00:00      2 drain* dn[031,037]
+extended-40core           up 7-00:00:00      1  drain dn061
+extended-40core           up 7-00:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+extended-40core           up 7-00:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
+extended-40core-shared    up 3-12:00:00      1  drain dn061
+extended-40core-shared    up 3-12:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+extended-40core-shared    up 3-12:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+extended-96core           up 7-00:00:00      1   plnd dg025
+extended-96core           up 7-00:00:00      1  drng@ dg023
+extended-96core           up 7-00:00:00      1   mix@ dg039
+extended-96core           up 7-00:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+extended-96core           up 7-00:00:00      1  down* dg009
+extended-96core           up 7-00:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+extended-96core-shared    up 3-12:00:00      1   plnd dg025
+extended-96core-shared    up 3-12:00:00      1  drng@ dg023
+extended-96core-shared    up 3-12:00:00      1   mix@ dg039
+extended-96core-shared    up 3-12:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+extended-96core-shared    up 3-12:00:00      1  down* dg009
+extended-96core-shared    up 3-12:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[046-048]
+hbm-1tb-long-96core       up 2-00:00:00      1   idle xm045
+hbm-extended-96core       up 7-00:00:00      3   plnd xm[008,021,088]
+hbm-extended-96core       up 7-00:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
+hbm-extended-96core       up 7-00:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
+hbm-large-96core          up    8:00:00      3   plnd xm[008,021,088]
+hbm-large-96core          up    8:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
+hbm-large-96core          up    8:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
+hbm-long-96core           up 2-00:00:00      3   plnd xm[008,021,088]
+hbm-long-96core           up 2-00:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
+hbm-long-96core           up 2-00:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
+hbm-medium-96core         up   12:00:00      3   plnd xm[008,021,088]
+hbm-medium-96core         up   12:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
+hbm-medium-96core         up   12:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
+hbm-short-96core          up    4:00:00      3   plnd xm[008,021,088]
+hbm-short-96core          up    4:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
+hbm-short-96core          up    4:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
+large-40core              up    8:00:00      2 drain* dn[031,037]
+large-40core              up    8:00:00      1  drain dn061
+large-40core              up    8:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+large-40core              up    8:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+large-96core              up    8:00:00      1   plnd dg025
+large-96core              up    8:00:00      1  drng@ dg023
+large-96core              up    8:00:00      1   mix@ dg039
+large-96core              up    8:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+large-96core              up    8:00:00      1  down* dg009
+large-96core              up    8:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+long-40core               up 2-00:00:00      2 drain* dn[031,037]
+long-40core               up 2-00:00:00      1  drain dn061
+long-40core               up 2-00:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+long-40core               up 2-00:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
+long-40core-shared        up 1-00:00:00      1  drain dn061
+long-40core-shared        up 1-00:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+long-40core-shared        up 1-00:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+long-96core               up 2-00:00:00      1   plnd dg025
+long-96core               up 2-00:00:00      1  drng@ dg023
+long-96core               up 2-00:00:00      1   mix@ dg039
+long-96core               up 2-00:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+long-96core               up 2-00:00:00      1  down* dg009
+long-96core               up 2-00:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+long-96core-shared        up 1-00:00:00      1   plnd dg025
+long-96core-shared        up 1-00:00:00      1  drng@ dg023
+long-96core-shared        up 1-00:00:00      1   mix@ dg039
+long-96core-shared        up 1-00:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+long-96core-shared        up 1-00:00:00      1  down* dg009
+long-96core-shared        up 1-00:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+medium-40core             up   12:00:00      2 drain* dn[031,037]
+medium-40core             up   12:00:00      1  drain dn061
+medium-40core             up   12:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+medium-40core             up   12:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+medium-96core             up   12:00:00      1   plnd dg025
+medium-96core             up   12:00:00      1  drng@ dg023
+medium-96core             up   12:00:00      1   mix@ dg039
+medium-96core             up   12:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+medium-96core             up   12:00:00      1  down* dg009
+medium-96core             up   12:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+ood-short-96core          up    4:00:00      1   idle dg038
+rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
+short-40core              up    4:00:00      2 drain* dn[031,037]
+short-40core              up    4:00:00      1  drain dn061
+short-40core              up    4:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+short-40core              up    4:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+short-40core-shared       up    4:00:00      2 drain* dn[031,037]
+short-40core-shared       up    4:00:00      1  drain dn061
+short-40core-shared       up    4:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
+short-40core-shared       up    4:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
+short-96core              up    4:00:00      1   plnd dg025
+short-96core              up    4:00:00      1  drng@ dg023
+short-96core              up    4:00:00      1   mix@ dg039
+short-96core              up    4:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+short-96core              up    4:00:00      1  down* dg009
+short-96core              up    4:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+short-96core-shared       up    4:00:00      1   plnd dg025
+short-96core-shared       up    4:00:00      1  drng@ dg023
+short-96core-shared       up    4:00:00      1   mix@ dg039
+short-96core-shared       up    4:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
+short-96core-shared       up    4:00:00      1  down* dg009
+short-96core-shared       up    4:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
+(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
+Press ENTER or type command to continue
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_ga_50.in  ga.sh
+(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
+(base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
+Submitted batch job 932640
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ ^C
+(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
+(base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
+Submitted batch job 932642
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
+(base) [ehspector@milan2 ga_run_50]$ scancel 932640
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
+(base) [ehspector@milan2 ga_run_50]$ scancel 932642
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_ga_50.in  ga.sh
+(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
+(base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
+Submitted batch job 932644
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto  R       0:03      1 dg038
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto  R       0:07      1 dg038
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0003.mol2  2w26_ga_50.in   vs_output.txt
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_50.out
+w26_5_ga.restart0002.mol2  2w26_5_ga.restart0005.mol2  ga.sh
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0006.mol2  ga.sh
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_50.in               vs_output.txt
+w26_5_ga.restart0002.mol2  2w26_5_ga.restart0005.mol2  2w26_ga_50.out
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0006.mol2  ga.sh
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_50.in               vs_output.txt
+w26_5_ga.restart0002.mol2  2w26_5_ga.restart0005.mol2  2w26_ga_50.out
+(base) [ehspector@milan2 ga_run_50]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto  R       0:41      1 dg038
+(base) [ehspector@milan2 ga_run_50]$ exit
+logout
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ class
+(base) [ehspector@milan2 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan2 AMS_536]$ check
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+ood-short 2w26_ga_ ehspecto  R       8:17      1 dg038
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  ga_run_50      test4.tar
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_2w26
+_gridbox          006_footprint  009_rescore         ga_run_5              Robs_new_2w26
+(base) [ehspector@milan2 2w26]$ cd ga_run_50/
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0008.mol2  2w26_5_ga.restart0016.mol2
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0009.mol2  2w26_5_ga.restart0017.mol2
+w26_5_ga.restart0002.mol2  2w26_5_ga.restart0010.mol2  2w26_5_ga.restart0018.mol2
+w26_5_ga.restart0003.mol2  2w26_5_ga.restart0011.mol2  2w26_ga_50.in
+w26_5_ga.restart0004.mol2  2w26_5_ga.restart0012.mol2  2w26_ga_50.out
+w26_5_ga.restart0005.mol2  2w26_5_ga.restart0013.mol2  ga.sh
+w26_5_ga.restart0006.mol2  2w26_5_ga.restart0014.mol2  vs_output.txt
+w26_5_ga.restart0007.mol2  2w26_5_ga.restart0015.mol2
+(base) [ehspector@milan2 ga_run_50]$ exit
+logout
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan2 ~]$ cd AMS_536/
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run_50/
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_5_ga.restart0000.mol2  2w26_5_ga.restart0019.mol2  2w26_5_ga.restart0038.mol2
+w26_5_ga.restart0001.mol2  2w26_5_ga.restart0020.mol2  2w26_5_ga.restart0039.mol2
+w26_5_ga.restart0002.mol2  2w26_5_ga.restart0021.mol2  2w26_5_ga.restart0040.mol2
+w26_5_ga.restart0003.mol2  2w26_5_ga.restart0022.mol2  2w26_5_ga.restart0041.mol2
+w26_5_ga.restart0004.mol2  2w26_5_ga.restart0023.mol2  2w26_5_ga.restart0042.mol2
+w26_5_ga.restart0005.mol2  2w26_5_ga.restart0024.mol2  2w26_5_ga.restart0043.mol2
+w26_5_ga.restart0006.mol2  2w26_5_ga.restart0025.mol2  2w26_5_ga.restart0044.mol2
+w26_5_ga.restart0007.mol2  2w26_5_ga.restart0026.mol2  2w26_5_ga.restart0045.mol2
+w26_5_ga.restart0008.mol2  2w26_5_ga.restart0027.mol2  2w26_5_ga.restart0046.mol2
+w26_5_ga.restart0009.mol2  2w26_5_ga.restart0028.mol2  2w26_5_ga.restart0047.mol2
+w26_5_ga.restart0010.mol2  2w26_5_ga.restart0029.mol2  2w26_5_ga.restart0048.mol2
+w26_5_ga.restart0011.mol2  2w26_5_ga.restart0030.mol2  2w26_5_ga.restart0049.mol2
+w26_5_ga.restart0012.mol2  2w26_5_ga.restart0031.mol2  2w26_5_ga.restart0050.mol2
+w26_5_ga.restart0013.mol2  2w26_5_ga.restart0032.mol2  2w26_ga_50.in
+w26_5_ga.restart0014.mol2  2w26_5_ga.restart0033.mol2  2w26_ga_50.out
+w26_5_ga.restart0015.mol2  2w26_5_ga.restart0034.mol2  ga.sh
+w26_5_ga.restart0016.mol2  2w26_5_ga.restart0035.mol2  vs_output.txt
+w26_5_ga.restart0017.mol2  2w26_5_ga.restart0036.mol2
+w26_5_ga.restart0018.mol2  2w26_5_ga.restart0037.mol2
+(base) [ehspector@milan2 ga_run_50]$ mkdir 50_generations
+(base) [ehspector@milan2 ga_run_50]$ mv *.mol2 50_generations/
+(base) [ehspector@milan2 ga_run_50]$ ls
+w26_ga_50.in  2w26_ga_50.out  50_generations  ga.sh  vs_output.txt
+(base) [ehspector@milan2 ga_run_50]$ cd 50_generations/
+(base) [ehspector@milan2 50_generations]$ cd ..
+(base) [ehspector@milan2 ga_run_50]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ga_run_5
+(base) [ehspector@milan2 ga_run_5]$ mkdir 5_generations
+(base) [ehspector@milan2 ga_run_5]$ mv *.mol2 5_generations/
+(base) [ehspector@milan2 ga_run_5]$ ls
+w26_ga_5.in  2w26_ga_5.out  5_generations
+(base) [ehspector@milan2 ga_run_5]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tut(base) [ehspect(base) [ehspector@m(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 (base) [ehspector@milan2 Tutorials]$ (base) [ehspector@milan(base) [(base) [ehspector@mila(base) [e(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutorials]$ client_loop: send disconnect: Broken pipe
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ home
+(base) [ehspector@milan1 espector]$ class
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  ga_run_50      test4.tar
+_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_2w26
+_gridbox          006_footprint  009_rescore         ga_run_5              Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd ga_calc/
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
+W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
+w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
+W26_fraglib_rigid.mol2     full_fraglib.dat
+W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
+(base) [ehspector@milan1 ga_calc]$ vi py.sh
+(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base(base) [ehspector@milan1 ga_c(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
+W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
+w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
+W26_fraglib_rigid.mol2     full_fraglib.dat
+W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
+(base) [ehspector@milan1 ga_calc]$ ls
+w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
+W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
+w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
+W26_fraglib_rigid.mol2     full_fraglib.dat
+W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
+(base) [ehspector@milan1 ga_calc]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ cd ga_run_5
+(base) [ehspector@milan1 ga_run_5]$ cd ..
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ cd ..
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ cd ../../
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd ../../
+(base) [ehspector@milan1 ~]$ ls
+AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
+(base) [ehspector@milan1 ~]$ cd AMS_536/
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd ../
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi commands.txt
+(base) [ehspector@milan1 AMS_536]$ touch make_folders
+(base) [ehspector@milan1 AMS_536]$ vi make_folders
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  make_folders  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ bash make_folders
+make_folders: line 3: folder: Is a directory
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  folder  make_folders  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd folder/
+(base) [ehspector@milan1 folder]$ ls
+(base) [ehspector@milan1 folder]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  folder  make_folders  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ rm -r folder/
+(base) [ehspector@milan1 AMS_536]$ rm make_folders
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd ..
+(base) [ehspector@milan1 ~]$ cd AMS_536/
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd ..
+(base) [ehspector@milan1 ~]$ cd ..
+(base) [ehspector@milan1 home]$ cd ..
+(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
+(base) [ehspector@milan1 bin]$ ls
+am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
+amberize_complex   espgen        nchemgrid_GB          showbox
+amberize_ligand    grid          nchemgrid_SA          showsphere
+amberize_receptor  grid-convert  parmcal               solvgrid
+antechamber        grid-convrds  parmchk               solvmap
+atomtype           make_phimap   prepare_amber.pl      sphere_selector
+bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
+chemgrid           mol2.py       prepgen               teLeap
+combine_torenv.py  mopac         resp                  tleap
+dock6              mopac.sh      respgen
+(base) [ehspector@milan1 bin]$ class
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 2w26/
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_50
+_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
+_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
+_energymin        008_cartesian_min   ga_run_5              test4.tar
+(base) [ehspector@milan1 2w26]$ mkdir de_novo
+(base) [ehspector@milan1 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_5       test4.tar
+_surface_spheres  006_footprint       2025_02_12a_test.tar  ga_run_50
+_gridbox          007_virtual_screen  de_novo               Robs_2w26
+_energymin        008_cartesian_min   ga_calc               Robs_new_2w26
+(base) [ehspector@milan1 2w26]$ cd ../../
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
+-bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
+-bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
+(base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/
+-bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
+(base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/
+-bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
+(base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
+-bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ cd
+(base) [ehspector@milan1 ~]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
+-bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory
+(base) [ehspector@milan1 ~]$ cd ..
+(base) [ehspector@milan1 home]$ cd ..
+(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
+(base) [ehspector@milan1 bin]$ ls
+am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
+amberize_complex   espgen        nchemgrid_GB          showbox
+amberize_ligand    grid          nchemgrid_SA          showsphere
+amberize_receptor  grid-convert  parmcal               solvgrid
+antechamber        grid-convrds  parmchk               solvmap
+atomtype           make_phimap   prepare_amber.pl      sphere_selector
+bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
+chemgrid           mol2.py       prepgen               teLeap
+combine_torenv.py  mopac         resp                  tleap
+dock6              mopac.sh      respgen
+(base) [ehspector@milan1 bin]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap
+(base) [ehspector@milan1 bin]$ class
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd ..
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ top
+top - 15:15:15 up 1 day,  2:11, 24 users,  load average: 0.72, 1.86, 3.46
+Tasks: 1532 total,   2 running, 1530 sleeping,   0 stopped,   0 zombie
+%Cpu(s):  0.8 us,  0.0 sy,  0.0 ni, 99.2 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
+MiB Mem : 515564.8 total, 495571.2 free,  20722.4 used,   2594.1 buff/cache
+MiB Swap:      0.0 total,      0.0 free,      0.0 used. 494842.4 avail Mem
+    PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND
+minkwan   20   0  164580  90868   3072 R  99.0   0.0   0:25.66 dock6
+ehspect+  20   0   23432   4096   3072 R   1.6   0.0   0:00.30 top
+root      20   0  259340  20196  16384 S   1.0   0.0   4:53.58 NetworkManager
+eswong    20   0  295692  13164   5120 S   0.5   0.0   0:11.35 code-e54c774e0a
+hborche+  20   0 4280208 284596  82944 S   0.5   0.1   0:01.07 cpptools-srv
+root      20   0  172980  12288   9216 S   0.0   0.0   0:40.57 systemd
+root      20   0       0      0      0 S   0.0   0.0   0:00.25 kthreadd
+root       0 -20       0      0      0 I   0.0   0.0   0:00.00 rcu_gp
+root       0 -20       0      0      0 I   0.0   0.0   0:00.00 rcu_par_gp
+root       0 -20       0      0      0 I   0.0   0.0   0:00.00 slub_flushwq
+root       0 -20       0      0      0 I   0.0   0.0   0:00.00 netns
+root       0 -20       0      0      0 I   0.0   0.0   0:00.00 kworker/0:0H-events+
+root       0 -20       0      0      0 I   0.0   0.0   0:00.00 mm_percpu_wq
+root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_kthre
+root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_rude_
+root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_trace
+root      20   0       0      0      0 S   0.0   0.0   0:00.38 ksoftirqd/0
+root      20   0       0      0      0 I   0.0   0.0   0:50.41 rcu_preempt
+root      rt   0       0      0      0 S   0.0   0.0   0:00.08 migration/0
+root     -51   0       0      0      0 S   0.0   0.0   0:00.00 idle_inject/0
+root      20   0       0      0      0 S   0.0   0.0   0:00.00 cpuhp/0
+root      20   0       0      0      0 S   0.0   0.0   0:00.00 cpuhp/1
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ cd ..
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan1 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) supremestudier@Evans-MBP Tutorial % ls
+O86		2w26		5EEN		folders.txt
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Permission denied, please try again.
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan1 AMS_536]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ vi ~/.bashrc
+(base) [ehspector@milan1 ~]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ~]$ home
+(base) [ehspector@milan2 espector]$ ls
+K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
+(base) [ehspector@milan2 espector]$ class
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/
+(base) [ehspector@milan2 2w26]$ ls
+_structure        005_dock            009_rescore           ga_run_5       test4.tar
+_surface_spheres  006_footprint       2025_02_12a_test.tar  ga_run_50
+_gridbox          007_virtual_screen  de_novo               Robs_2w26
+_energymin        008_cartesian_min   ga_calc               Robs_new_2w26
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ mkdir de_novo
+(base) [ehspector@milan2 1O86]$ cd de_novo/
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2
+(base) [ehspector@milan2 de_novo]$ touch Du.in
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in
+(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in
+--------------------------------------
+DOCK v6.12
+Released September 2024
+Copyright UCSF
+--------------------------------------
+Conformational Sampling Parameters
+------------------------------------------------------------------------------------------
+                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):denovo
+De Novo Build Parameters
+------------------------------------------------------------------------------------------
+                                     dn_fraglib_scaffold_file [fraglib_scaffold.mol2] ():
+                                       dn_fraglib_linker_file [fraglib_linker.mol2] ():
+                                    dn_fraglib_sidechain_file [fraglib_sidechain.mol2] ():
+                                     dn_user_specified_anchor [yes] (yes no):
+                                       dn_fraglib_anchor_file [fraglib_anchor.mol2] ():
+                                              dn_torenv_table [fraglib_torenv.dat] ():
+                                           dn_name_identifier [denovo] ():
+                                           dn_sampling_method [graph] (ex | rand | graph):
+                                           dn_graph_max_picks [30] ():
+                                             dn_graph_breadth [3] ():
+                                               dn_graph_depth [2] ():
+                                         dn_graph_temperature [100.0] ():
+                            dn_pruning_conformer_score_cutoff [100.0] ():
+                    dn_pruning_conformer_score_scaling_factor [2.0] ():
+                                 dn_pruning_clustering_cutoff [100.0] ():
+                                         dn_remove_duplicates [yes] ( no | yes):
+                                    dn_max_duplicates_per_mol [0] ():
+                                   dn_write_pruned_duplicates [no] ( no | yes ):
+                                          dn_advanced_pruning [yes] (yes | no):
+                                      dn_prune_initial_sample [yes] (yes | no):
+                                           dn_sample_torsions [yes] (yes | no):
+                                 dn_prune_individual_torsions [yes] (yes | no):
+                                   dn_prune_combined_torsions [yes] (yes | no):
+                                     dn_random_root_selection [no] (yes | no):
+                                        dn_mol_wt_cutoff_type [soft] (hard | soft):
+                                   dn_upper_constraint_mol_wt [550.0] ():500
+                                   dn_lower_constraint_mol_wt [0.0] ():
+                                            dn_mol_wt_std_dev [35.0] ():
+                                        dn_constraint_rot_bon [15] ():
+                                  dn_constraint_formal_charge [2.0] ():
+                                        dn_heur_unmatched_num [1] ():
+                                         dn_heur_matched_rmsd [2.0] ():
+                                            dn_unique_anchors [1] ():
+                                           dn_max_grow_layers [9] ():
+                                             dn_max_root_size [25] ():
+                                            dn_max_layer_size [25] ():
+                                           dn_max_current_aps [5] ():
+                                   dn_max_scaffolds_per_layer [1] ():
+                               dn_max_successful_att_per_root [50000] ():
+                                         dn_write_checkpoints [yes] (yes no):
+                                          dn_write_prune_dump [yes] (yes no):
+                                             dn_write_orients [no] (yes no):
+                                        dn_write_growth_trees [no] (yes no):
+                                             dn_output_prefix [output] ():
+Internal Energy Parameters
+------------------------------------------------------------------------------------------
+                                          use_internal_energy [yes] (yes no):
+                                      internal_energy_rep_exp [12] ():
+                                       internal_energy_cutoff [100.0] ():
+Note: Internal energy only includes repulsive VDW for growth and/or minimization.
+Database Filter Parameters
+------------------------------------------------------------------------------------------
+                                          use_database_filter [no] (yes no):
+Orient Ligand Parameters
+------------------------------------------------------------------------------------------
+                                                orient_ligand [yes] (yes no):no
+Bump Filter Parameters
+------------------------------------------------------------------------------------------
+                                                  bump_filter [no] (yes no):
+Master Score Parameters
+------------------------------------------------------------------------------------------
+                                              score_molecules [yes] (yes no):
+Contact Score Parameters
+------------------------------------------------------------------------------------------
+                                        contact_score_primary [no] (yes no):
+Grid Score Parameters
+------------------------------------------------------------------------------------------
+                                           grid_score_primary [yes] (yes no):
+                                     grid_score_rep_rad_scale [1] ():
+                                         grid_score_vdw_scale [1] ():
+                                          grid_score_es_scale [1] ():
+                                          grid_lig_efficiency [no] (yes no):
+                                       grid_score_grid_prefix [grid] ():
+GIST Score Parameters
+------------------------------------------------------------------------------------------
+MultiGrid Score Parameters
+------------------------------------------------------------------------------------------
+Dock3.5 Score Parameters
+------------------------------------------------------------------------------------------
+Continuous Energy Score Parameters
+------------------------------------------------------------------------------------------
+Footprint Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Pharmacophore Similarity Score Parameters
+------------------------------------------------------------------------------------------
+Hbond Energy Score Parameters
+------------------------------------------------------------------------------------------
+Internal Energy Score Parameters
+------------------------------------------------------------------------------------------
+Descriptor Score Parameters
+------------------------------------------------------------------------------------------
+Zou GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+Hawkins GB/SA Score Parameters
+------------------------------------------------------------------------------------------
+SASA Score Parameters
+------------------------------------------------------------------------------------------
+Amber Score Parameters
+------------------------------------------------------------------------------------------
+Simplex Minimization Parameters
+------------------------------------------------------------------------------------------
+                                              minimize_ligand [yes] (yes no):
+                                              minimize_anchor [yes] (yes no):
+                                     minimize_flexible_growth [yes] (yes no):
+                              use_advanced_simplex_parameters [no] (yes no):
+                                           simplex_max_cycles [1] ():
+                                       simplex_score_converge [0.1] ():
+                                       simplex_cycle_converge [1.0] ():
+                                           simplex_trans_step [1.0] ():
+                                             simplex_rot_step [0.1] ():
+                                            simplex_tors_step [10.0] ():
+                                simplex_anchor_max_iterations [500] ():
+                                  simplex_grow_max_iterations [500] ():
+                          simplex_grow_tors_premin_iterations [0] ():
+                                            simplex_final_min [no] (yes no):
+                                          simplex_random_seed [0] ():
+                                        simplex_restraint_min [no] (yes no):
+Atom Typing Parameters
+------------------------------------------------------------------------------------------
+                                                   atom_model [all] (all | united):
+                                                vdw_defn_file [vdw.defn] ():
+                                               flex_defn_file [flex.defn] ():
+                                              flex_drive_file [flex_drive.tbl] ():
+------------------------------------------------------------------------------------------
+Initializing De Novo Growth Routines...
+ Reading the scaffold library from fraglib_scaffold.mol2...Could not open fraglib_scaffold.mol2. Program will terminate.
+No such file or directory(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ cd ../../
+(base) [ehspector@milan2 Tutorials]$ cd ../
+(base) [ehspector@milan2 AMS_536]$ ls
+class_project  commands.txt  Notes.txt  Tutorials
+(base) [ehspector@milan2 AMS_536]$ vi Notes.txt
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in
+(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
+/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
+(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99
+ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99': No such file or directory
+(base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw
+ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw': No such file or directory
+(base) [ehspector@milan2 de_novo]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/
+(base) [ehspector@milan2 parameters]$ ls
+                         fraglib_linker.mol2         prot.table.ambcrg.sybH
+antechamber               fraglib_scaffold.mol2       sa_fraglib.dat
+chem.defn                 fraglib_sidechain.mol2      screen.in
+chemgrid                  fraglib_torenv.dat          screen.para
+chem_match.tbl            leap                        vdw_AMBER_parm94.defn
+flex.defn                 na.table.ambcrg             vdw_AMBER_parm94.dock3_7.defn
+flex_drive_mod.tbl        pains_table_2019_09_01.dat  vdw_AMBER_parm94.dock3_7_one_C_3.defn
+flex_drive.tbl            pains_table.dat             vdw_AMBER_parm96.defn
+flex_just_OH.defn         ph4.defn                    vdw_AMBER_parm99.defn
+flex_mod2.defn            prot.table.ambcrg.ambH      vdw_de_novo.defn
+flex_mod.defn             prot.table.ambcrg.pdb3H     vdw.parms.amb
+fraglib_ga_scaffold.mol2  prot.table.ambcrg.pdbH      vdw.parms.update.amb
+(base) [ehspector@milan2 parameters]$ class
+(base) [ehspector@milan2 AMS_536]$ cd ls
+-bash: cd: ls: No such file or directory
+(base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/
+(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out
+(base) [ehspector@milan2 de_novo]$ vi Du.out
+(base) [ehspector@milan2 de_novo]$ cd ..
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore   de_novo
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 2w26/ga_calc/
+(base) [ehspector@milan2 ga_calc]$ ;s
+-bash: syntax error near unexpected token `;'
+(base) [ehspector@milan2 ga_calc]$ ls
+w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
+W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
+w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
+W26_fraglib_rigid.mol2     full_fraglib.dat
+W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
+(base) [ehspector@milan2 ga_calc]$ vi 2w26_fraglib.in
+(base) [ehspector@milan2 ga_calc]$ cd ..
+(base) [ehspector@milan2 2w26]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ mkdir ga_calc
+(base) [ehspector@milan2 1O86]$ cd ..
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/2w26_fraglib.in 1O86/ga_calc/1O86_fraglib.in
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/lib.sh 1O86/ga_calc/lib.sh
+(base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/py.sh 1O86/ga_calc/py.sh
+(base) [ehspector@milan2 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan2 Tutorials]$ cd 1O86/
+(base) [ehspector@milan2 1O86]$ ls
+_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore   de_novo
+_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt  ga_calc
+(base) [ehspector@milan2 1O86]$ cd ga_calc/
+(base) [ehspector@milan2 ga_calc]$ ls
+O86_fraglib.in  lib.sh  py.sh
+(base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.in
+(base) [ehspector@milan2 ga_calc]$ vi lib.sh
+(base) [ehspector@milan2 ga_calc]$ bash lib.sh
+(base) [ehspector@milan2 ga_calc]$ ls
+O86_fraglib.in           1O86_fraglib_rigid.mol2     1O86_fraglib_sidechain.mol2  py.sh
+O86_fraglib_linker.mol2  1O86_fraglib_scaffold.mol2  1O86_fraglib_torenv.dat
+O86_fraglib.out          1O86_fraglib_scored.mol2    lib.sh
+(base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.out
+(base) [ehspector@milan2 ga_calc]$ ls
+O86_fraglib.in           1O86_fraglib_rigid.mol2     1O86_fraglib_sidechain.mol2  py.sh
+O86_fraglib_linker.mol2  1O86_fraglib_scaffold.mol2  1O86_fraglib_torenv.dat
+O86_fraglib.out          1O86_fraglib_scored.mol2    lib.sh
+(base) [ehspector@milan2 ga_calc]$ vi py.sh
+(base) [ehspector@milan2 ga_calc]$ module list
+Currently Loaded Modulefiles:
+) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack
+) shared                   4) mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan2 ga_calc]$ module load python
+(base) [ehspector@milan2 ga_calc]$ bash py.sh
+(base) [ehspector@milan2 ga_calc]$ ls
+O86_fraglib.in             1O86_fraglib_scored.mol2     lib.sh
+O86_fraglib_linker.mol2    1O86_fraglib_sidechain.mol2  py.sh
+O86_fraglib.out            1O86_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
+O86_fraglib_rigid.mol2     full_fraglib.dat
+O86_fraglib_scaffold.mol2  full_sorted_fraglib.dat
+(base) [ehspector@milan2 ga_calc]$ pwd
+/gpfs/home/ehspector/AMS_536/Tutorials/1O86/ga_calc
+(base) [ehspector@milan2 ga_calc]$ cd ../de_novo/
+(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out
+(base) [ehspector@milan2 de_novo]$ vi Du.out
+(base) [ehspector@milan2 de_novo]$ vi Du.in
+(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
+Segmentation fault (core dumped)
+(base) [ehspector@milan2 de_novo]$ la
+-bash: la: command not found
+(base) [ehspector@milan2 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
+(base) [ehspector@milan2 de_novo]$ vi Du.out
+(base) [ehspector@milan2 de_novo]$ vi 1O86_ligand_Du.mol2
+(base) [ehspector@milan2 de_novo]$ exit
+logout
+Connection to milan.seawulf.stonybrook.edu closed.
+(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
+ehspector@milan.seawulf.stonybrook.edu's password:
+Duo two-factor login for ehspector
+Enter a passcode or select one of the following options:
+. Duo Push to XXX-XXX-9204
+Passcode or option (1-1): 1
+Pushed a login request to your device...
+Success. Logging you in...
+Loading gcc-stack
+  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
+(base) [ehspector@milan1 ~]$ class
+(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
+(base) [ehspector@milan1 Tutorials]$ ls
+O86  2w26  5EEN
+(base) [ehspector@milan1 Tutorials]$ cd 1O86/de_novo/
+(base) [ehspector@milan1 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ vi Du.out
+(base) [ehspector@milan1 de_novo]$ vi Du.in
+(base) [ehspector@milan1 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
+Segmentation fault (core dumped)
+(base) [ehspector@milan1 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ vi Du.out
+(base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ vi Du.out
+(base) [ehspector@milan1 de_novo]$ vi 1O86_ligand_Du.mol2
+(base) [ehspector@milan1 de_novo]$ rm 1O86_ligand_Du.mol2
+(base) [ehspector@milan1 de_novo]$ ls
+Du.in  Du.out  Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ rm Du.out
+(base) [ehspector@milan1 de_novo]$ ls
+O86_ligand_Du.mol2  Du.in  Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
+(base) [ehspector@milan1 de_novo]$ ls
+O86_ligand_Du.mol2  Du.out                             Du.out.completed.denovo_build.mol2
+Du.in                Du.out.anchor_1.root_layer_1.mol2  Du.out.denovo_build.mol2
+(base) [ehspector@milan1 de_novo]$ vi Du.out
+(base) [ehspector@milan1 de_novo]$ vi Du.in
+conformer_search_type                                        denovo
+dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
+dn_fraglib_linker_file                                       /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_linker.mol2
+dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
+dn_user_specified_anchor                                     yes
+dn_fraglib_anchor_file                                       1O86_ligand_Du.mol2
+dn_torenv_table                                              ../ga_calc/unique_full_sorted_fraglib.dat
+dn_name_identifier                                           denovo
+dn_sampling_method                                           graph
+dn_graph_max_picks                                           30
+dn_graph_breadth                                             3
+dn_graph_depth                                               2
+dn_graph_temperature                                         100.0
+dn_pruning_conformer_score_cutoff                            100.0
+dn_pruning_conformer_score_scaling_factor                    2.0
+dn_pruning_clustering_cutoff                                 100.0
+dn_remove_duplicates                                         yes
+dn_max_duplicates_per_mol                                    0
+dn_write_pruned_duplicates                                   no
+dn_advanced_pruning                                          yes
+dn_prune_initial_sample                                      yes
+dn_sample_torsions                                           yes
+dn_prune_individual_torsions                                 yes
+dn_prune_combined_torsions                                   yes
+dn_random_root_selection                                     no
+dn_mol_wt_cutoff_type                                        soft
+dn_upper_constraint_mol_wt                                   1000
+dn_lower_constraint_mol_wt                                   0.0
+dn_mol_wt_std_dev                                            35.0
+dn_constraint_rot_bon                                        15
+dn_constraint_formal_charge                                  2.0
+dn_heur_unmatched_num                                        1
+dn_heur_matched_rmsd                                         2.0
+dn_unique_anchors                                            1
+dn_max_grow_layers                                           1
+dn_max_root_size                                             25
+dn_max_layer_size                                            25
+dn_max_current_aps                                           5
+dn_max_scaffolds_per_layer                                   1
+dn_max_successful_att_per_root                               50000
+dn_write_checkpoints                                         yes
+dn_write_prune_dump                                          yes
+dn_write_orients                                             no
+dn_write_growth_trees                                        no
+dn_output_prefix                                             Du.out
+use_internal_energy                                          yes
+internal_energy_rep_exp                                      12
+internal_energy_cutoff                                       100.0
+use_database_filter                                          no
+orient_ligand                                                no
+bump_filter                                                  no
+score_molecules                                              yes
+contact_score_primary                                        no
+grid_score_primary                                           yes
+grid_score_rep_rad_scale                                     1
+grid_score_vdw_scale                                         1
+grid_score_es_scale                                          1
+grid_lig_efficiency                                          no
+grid_score_grid_prefix                                       ../003_gridbox/grid
+minimize_ligand                                              yes
+minimize_anchor                                              yes
+minimize_flexible_growth                                     yes
+use_advanced_simplex_parameters                              no
+simplex_max_cycles                                           1
+simplex_score_converge                                       0.1
+simplex_cycle_converge                                       1.0
+simplex_trans_step                                           1.0
+simplex_rot_step                                             0.1
+simplex_tors_step                                            10.0
+simplex_anchor_max_iterations                                500
+simplex_grow_max_iterations                                  500
+simplex_grow_tors_premin_iterations                          0
+simplex_final_min                                            no
+simplex_random_seed                                          0
+simplex_restraint_min                                        no
+atom_model                                                   all
+vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
+flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl