2025 DOCK tutorial 1 with PDBID 1O86

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

Last login: Sat Jan 25 20:39:22 on ttys000 (base) supremestudier@Evans-MBP ~ % ls 1ay7.cif 1dqx.cif 2012-sat-results.csv 4ees.cif 5tj3.cif 6fev.cif 7rfw.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:

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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
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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
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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)

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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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 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

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:

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:

1. 0 0x7ffff7d59e39 in formatted_transfer_scalar_read

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

1. 1 0x7ffff7d5b535 in formatted_transfer

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

1. 2 0x4049e0 in ???
2. 3 0x40516a in ???
3. 4 0x40117c in ???
4. 5 0x7ffff742958f in ???
5. 6 0x7ffff742963f in ???
6. 7 0x4011b4 in ???
7. 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:

1. 0 0x7ffff7d54ca5 in already_open

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

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

1. 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 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 beckert hkamran lpanwang rkhanal xbarron 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 cjbyrnes jelau mkhemchandan sgoswami yusjin 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 2017 2019 2021 2023 2025 junk.txt zzz.programs 2018 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 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@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 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:

1. 0 0x7ffff7d54ca5 in already_open

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

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

1. 0 0x7ffff7d54ca5 in already_open

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

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

1. 0 0x7ffff7d54ca5 in already_open

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

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

1. 0 0x7ffff7d54ca5 in already_open

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

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

1. 0 0x7ffff7d59e39 in formatted_transfer_scalar_read

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

1. 1 0x7ffff7d5b535 in formatted_transfer

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

1. 2 0x4049e0 in ???
2. 3 0x40516a in ???
3. 4 0x40117c in ???
4. 5 0x7ffff742958f in ???
5. 6 0x7ffff742963f in ???
6. 7 0x4011b4 in ???
7. 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:

1. 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:

1. 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

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 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

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 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

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DOCK v6.12

Released September 2024 Copyright UCSF

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Conformational Sampling Parameters

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

De Novo Build Parameters

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                                    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

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                                         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

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                                         use_database_filter [no] (yes no):

Orient Ligand Parameters

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                                               orient_ligand [yes] (yes no):no

Bump Filter Parameters

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                                                 bump_filter [no] (yes no):

Master Score Parameters

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                                             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

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MultiGrid Score Parameters

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Dock3.5 Score Parameters

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Continuous Energy Score Parameters

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Footprint Similarity Score Parameters

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Pharmacophore Similarity Score Parameters

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Hbond Energy Score Parameters

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Internal Energy Score Parameters

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Descriptor Score Parameters

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Zou GB/SA Score Parameters

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Hawkins GB/SA Score Parameters

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SASA Score Parameters

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Amber Score Parameters

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Simplex Minimization Parameters

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                                             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

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

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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