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

Latest revision as of 13:41, 13 May 2025

1 DOCK Tutorial using PDB 1O86
2 000: Foundations
3 001: Structure Prep
4 002: Spheres
- 4.1 Generate the Required Surface File
- 4.2 Selecting Spheres Localized on Binding Site
5 003: Grid/box
- 5.1 Generating the Box
- 5.2 Generating the Grid
6 004: Minimization
7 005: Rigid Docking
8 006: Flexible Docking
9 007: Footprint Scoring
10 008: 5K Virtual Screening
11 009: Genetic Algorithm
12 010: De Novo Design Example
13 Running a Generic De Novo Calculation

DOCK Tutorial using PDB 1O86

This tutorial is a series of modules designed to familiarize a new user with the basic functions and features of DOCK6, as well as provide guidance on its execution and analysis of results. Modules should be read in a linear fashion, as each module builds on the prior one.

The the full DOCK manual contains much more information than this tutorial, and as such is recommended as a resource if the information provided herein proves unsatisfactory.

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.

Seawulf

To complete this tutorial as a Stony Brook student, you will need an account on Seawulf. A ticket to obtain an account can be submitted on the Seawulf website; Dr. Rizzo will need to provide approval for account activation.

The Seawulf website also has a list of best practices for using a High Performance Computing (HPC) cluster. We recommend reading through them before attempting to run any intensive programs on Seawulf. Of particular note is the job management system SLURM - we provide a full tutorial on this system in section 008 of this tutorial if you want to read up on it now, but it will not be necessary for this tutorial until that point.

SSH

You will need to use a Secure Shell (SSH) connection to connect to Seawulf remotely. A guide to this process is available on the Seawulf website.

Basic Unix Commands and Environment

Seawulf uses a terminal-based Unix operating system. If you have never used a terminal-based OS before, you should familiarize yourself with some basic Unix tutorials. Broadly, you should know how to:

List your working directory with pwd, change your working directory with cd, make new directories with mkdir, remove directories with rmdir, and list the contents of a directory with ls
Edit files using the text editor vim (use the vimtutor to read about basic functionality)
Create an empty file with touch, move files and directories around with mv, copy directories and files with cp, and (very carefully!) remove directories and files with rm
Determine if commands are available with which
Understand how to use commands and how flags/input parameters should be formatted

You should also understand the concept of filepaths, and how they are used by commands. Much of DOCK relies on you using the correct filepaths to pass files and parameters into the program, and if the paths are wrong, then the program will not work. When possible, it is advisable to use absolute filepaths (paths that start at the root directory), as opposed to paths relative to your current working directory. For example, if you are in the directory /gpfs/home/yourusername/tutorial/002_spheres, referencing the absolute path /gpfs/home/yourusername/tutorial/001_structure/important_structure.pdb for a needed structure file is more reliable than the relative path ../001_structure/important_structure.pdb, as the latter path is relative to 002_spheres/, and meaningless outside of that context. The command realpathwill return the absolute path of any file passed to it, which is useful for quickly and accurately determining the absolute path of any file.

To work with DOCK6, it may also be necessary to add a path to your config file that tells Unix where to look for DOCK-related commands. You can check if you need to do this using the command which dock6. If which informs you that no dock6 can be found, you will need to edit your .bashrc file:

Move to your home directory by either entering cd or cd ~
Use the command vi .bashrc to start editing your personal config file
At the bottom of the file, add the following line:

export PATH=$PATH:/Path/To/Your/DOCK6/bin

where Path/To/Your/DOCK6/ should be replaced with whatever the path is to your local DOCK installation (note: the full path should end with /bin). At the time of this writing, there is a compiled version of DOCK6.12 at /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/, but if this does not work then ask Dr. Rizzo or a lab member where a compiled instance can be found

4. Save and exit the file, then enter the command source .bashrc into the terminal.

5. Now when you request which dock6, the terminal should return the path to the directory you just provided.

After all this, you should have a good understanding of how to navigate the Unix terminal, and have the DOCK6 suite ready to use in your environment.

SCP File Transfer

Another important aspect of working on Seawulf is uploading and downloading files to your local machine. This is accomplished using the Secure Copy Protocol (scp) terminal command. See the pertinent section on the Seawulf website. For Windows, it may be advisable to download a third party program; FileZilla works for this task.

Directory setup

Finally, assuming all necessary base Unix knowledge has been obtained, you will want to set up a set of directories for the work you will be doing in this tutorial. The directories will help you compartmentalize your work and help to prevent important files from being overwritten or lost. For the modules of this tutorial, we recommend setting up this directory structure, and setting up folders on your local machine with the same names for ease of file transfer:

First, create a tutorial directory in your home directory:

cd ~
mkdir tutorial

Then, make a series of subdirectories inside of that tutorial directory:

cd ~/tutorial
mkdir 001_structure
mkdir 002_spheres
mkdir 003_gridbox
mkdir 004_energy_min
mkdir 005_rigid_dock
mkdir 006_flex_dock
mkdir 007_footprint
mkdir 008_virtual_screen
mkdir 009_gen_alg
mkdir 010_de_novo

A Note on Troubleshooting

Finally, despite our best efforts at accuracy, a healthy amount of this tutorial will likely not go smoothly for you. There will be errors and inconsistencies between what you see here and what happens on Seawulf, and there may not be an immediate answer for what you should do to fix them. The instinct when this happens is to find someone who knows what might have happened and ask them for advice, and while this will usually be helpful, it may be inefficient. As such, we advise you to first please troubleshoot. No program you will use in this tutorial is intended to be a black box. All of them do their best to return errors that tell you what is going wrong, and where to look to fix it. If you get an error, read it! Often it will tell you that it can't find a particular file ("doesn't exist" is the favorite wording), or that some piece of the input is giving it trouble— these tell you what paths to check or lines of a file to review. Also, copy-pasting an entire error into Google (or ChatGPT if you must) is a completely valid line of inquiry, and often yields helpful results.

Having said that, here are some common errors and tactics you can use to fix them:

"[File] could not be opened" or "[file] does not exist" usually indicates that a path you gave the program is not accurate. You can "sanity check" paths by copying them directly from the input and putting them into an ls command. If it throws an error, fix the path!

"version `GLIBCXX_whatever' not found" is generally an issue with how the DOCK installation was compiled. Try to find a different version (/gpfs/projects/AMS536/zzz.programs usually has several versions available) or try running the command on a different node (Milan or Login)

Errors mentioning FORTRAAN: Make sure the input files are named correctly(ex INSPH for sphgen) and there are no extra spaces or lines anywhere in the input files. Sometimes they sneak in at the start or end of a line and are parsed literally.

Often, output is sent into a .out file instead of written to the console. If the program terminates immediately but does not return expected files, check whatever .out file was written for errors at the very bottom.

001: Structure Prep

Downloading the PDB

Having setup your necessary environment to work on Seawulf, let's navigate to your local computer and begin the protein preparation process:

To begin protein preparation you will need the 1O86 PDB file. 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 dropdown menu will appear on the screen:

Select 'Legacy PDB Format'. Now the PDB file should be downloaded to your local computer.

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

Protein Isolation

Now that you have the downloaded PDB, the first step is to isolate and modify our protein, if necessary.

First, open the PDB in Chimera using File >> Open, zoom into where the ligand is, hold the control key and click to select an atom on the ligand, and press the up arrow key to highlight the ligand. Then go to Actions >> Focus.

The ligand should now be highlighted in green; you will see it is surrounded by water molecules:

We're going to get rid of the ligand and the water molecules.

First, since the ligand is highlighted, go to Actions >> Atoms/Bonds >> Delete.

There may be a glycine molecule remaining in the binding pocket. For the sake of simplicity, we are going to delete this as well. Control+click to select an atom in the glycine, up arrow to highlight the whole molecule, and Actions >> Atoms/Bonds >> Delete it in the same manner as the ligand.

Next, to get rid of the water molecules, navigate to Select >> Residue >> HOH

You'll notice that all of the water molecules are highlighted:

Just like the ligand, navigate to Actions >> Atoms/Bonds >> Delete

Now you have just a protein:

Inspecting the Protein

With just the protein file, lets inspect if there are any missing loops along the exterior. First, to make the view clearer, go to View >> Focus again to put the whole protein in focus.

You'll notice that there is a missing loop between residues 434 and 439.

To refine the missing loop, go to Tools >> Structure Editing >> select Model/Refine Loops

The following pop up menus will appear:

This is a list of the residues in the protein. The residues 435-438 boxed in red denote the ones involved with the missing loop.

This is the Modeller/Refine Menu. If you have not used it before, the Modeller License Key field may be empty, which will prevent the program from running. You will first need to register for a Modeller key on the official page. They will email you with the registration key relatively promptly (within a day but usually sooner). Note that because this program connects to a webserver for the loop modeling, you will require a stable internet connection to use it.

You can leave all the other options selected as is. Once you select apply, wait a couple of minutes. The program is generating different refinements to the missing loops. The residue menu will say "Running Modeller Web Service". Additionally, you'll be able to track the process completed on the search bar menu on the bottom part of the screen on Chimera.

Once the modeler is 100% completed, the following popup menu will appear on Chimera:

You can see that the modeller program generated five alternative protein models that refined the missing loop. If you press the shift key and highlight all of the model numbers you will see the following proteins with fixed loops.

Now, using the drop down menu, from earlier, you'll want to assess what's the best model to choose that has refined loops. Sometimes the difference in scores are negligible and you may want to select based on zDope, which would mean any loop is sufficient. However, there may be another score that could narrow your decision making.

In the 'Modeller Results' menu, select Fetch Scores. You'll see in your chimera window that a job was submitted. This is signaling to the program to retrieve the scores from the program. Once the job is finished, the Estimated RMSD and Estimated Overlap columns will contain values:

From adding more scores, you'll notice that the models differ in their Estimated RMSD values. Based on these values, Models 1.2 or 1.5 are a good choice based on RMSD. So, let's choose model 1.2 as our protein model to use in this tutorial. We will also save this model as our new PDB file.

Go to File >> Save PDB. When the save menu appears, make sure that only the second model is selected like so:

Let's also give this PDB a new title, the one supplied is 1O86_fixed_protein.pdb . Additionally, we will need the original PDB for ligand preparation.

Press save and now you have a refined protein to prepare.

Protein Preparation

After saving a protein with modelled loops as a PDB, use File >> Close Session to clear your Chimera session. Then, File >> Open the 1O86_fixed_protein.pdb

In order to use this protein for docking calculations, we will need to generate a charged, protonated protein and ligand files. Charged molecules must be saved in Mol2 format, as the PDB file format does not support partial atomic charges.

We will first save a version of the protein in Mol2 format that does not have any charges or hydrogens. Go to File >> Save Mol2. You will want to give this mol2 file a title that describes the fact that the protein doesn't have hydrogens or charges. So let's name this file 1O86_protein_nH_ncH.mol2

The nH refers to "no hydrogens" and the ncH refers to "no charges".

Now that the mol2 is saved, we can protonate and charge the receptor in preparation for docking.

Adding Hydrogens

Go to Tools >> Structure Editing >> AddH

The following menu will appear:

All the defaults that are selected are acceptable. Select OK.

You will get a confirmation message on the chimera text bar that says 'Hydrogens Added'. Now you have added hydrogens to the protein file. The last thing to do is to add charges.

Adding Charges

Before we can save the second mol2 for the protein we must also add charges to the protein.

Go to Tools >> Structure Editing >> press Add Charge

The following menu will appear:

By default Chimera selects AM1-BCC charges, but for this tutorial we are going to use Gasteiger charges. Every other selection on the menu is okay, so after changing the charge type, go ahead and select apply. You'll notice another pop up menu appears:

This deals with ions. Just as before, make sure that Gasteiger is selected. All other defaults are okay. Select OK. The Chimera window will inform you that standard charges are added.

Now that your protein has hydrogens and charges, we can go ahead and generate the second mol2 file.

Go to File >> Save Mol2. This time the name should reflect that the protein has hydrogens and charges. Let's name it 1O86_protein_wH_wcH.mol2 .

Now our protein files are prepared for docking, let's now turn our attention to preparing the ligand.

Isolating the Ligand

Having made a Protein PDB and generated two mol2 files, lets now do the same thing for the ligand. The first step is to File >> Close Session to clear the current environment, then open the original PDB file that we downloaded.

Just like in the protein section, press control and select an atom on the ligand. Then press the up arrow to highlight the entire ligand:

Go to Select >> Invert (selected models)

You'll notice that everything around the ligand is highlighted.

Now go to Actions >> Atoms/Bonds >> delete

Now we have a file that just contains the ligand.

Go to File >> Save PDB and name the file 1O86_ligand.pdb

This will be the file that we will use to prepare the mol2 files for the dock program.

You can now close your current session on Chimera by going to File >> Close Session

Preparing the Ligand

Now that we have a ligand only PDB, lets go ahead and generate the two mol2 files with the ligand.

The first step is to go to open the 1O86_ligand.pdb on chimera.

Go to File >> Save Mol2

Lets give the title of this first mol2 to denote no hydrogens or charge on the ligand.

Call it 1O86_ligand_nH_ncH.mol2

Running Dock Prep

To generate the second mol2 you are more than welcome to revisit the steps taken to generate the second protein mol2. In the case of the ligand, we will introduce an alternative with a program called Dock Prep.

First, return to 1O86_ligand.pdb on chimera:

Go to Tools >> Structure Editing >> DockPrep

The following pop-up menu will appear:

All of the default parameters are sufficient. Select OK.

The next set of drop down menus will be the same as adding hydrogens and charges to a protein.

Remember all of the defaults are okay for adding hydrogens, but make sure you switch from

AM1-BCC to Gasteiger charges when adding the charges for the ligand.

All other defaults are sufficient for each of the other pop-up menus.

The following images show the pop-up menus that will appear after you accept using Dock Prep and contain the acceptable defaults:

The Hydrogen Menu

The Charge Menu

The Net Charge Menu

What's neat about Dock Prep is that the last pop-up menu will be the Save Mol2 menu:

Lets give this mol2 a file name that specifies that it has hydrogens and charges.

Call it 1O86_ligand_wH_wcH.mol2

Congratulations, you've generated all the necessary mol2 files to advance to the next steps of this tutorial.

Lets transfer the mol2 files onto seawulf using the following command

  scp *mol2 yourusername@stonybrook.edu:'/gpfs/home/yourusername/tutorial/001_structure'

002: Spheres

Generate the Required Surface File

Open the 1O86_protein_nH_ncH.mol2 (with no hydrogens, no charges) in Chimera and hit Actions >> Surface >> Show
Write the DMS file by choosing Tools > Structure Editing > Write DMS; save the file as 1O86.dms
Upload the DMS file to your ~/tutorial/002_spheres directory on Seawulf using scp
Now, move to the Seawulf terminal interface and navigate to your ~/tutorial/002_spheres directory. Create a sphgen input file using the following command:

vi INSPH

5. Paste the following into your input file, ensuring that no additional lines are pasted:

./1O86.dms
R
X
0.0
4.0
1.4
1O86.sph

6. Run the program with the following command

sphgen -i INSPH -o OUTSPH

7. Download the output file to your local directory and File >> Open it in the same scene as your protein file in Chimera. This will overlay the generated spheres on the protein.

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

Selecting Spheres Localized on Binding Site

Run program on dock 6 called sphere_selector:

sphere_selector 1O86.sph ../001_structure/1O86_ligand_nH_ncH.mol2 10.0

2. Output file will automatically be written as selected_spheres.sph

3. Download this file to your local computer and overlay the file with your original protein file to ensure the spheres are localized over your ligand in the same manner as the 1O86.sph file in the previous step.

4. Select and hide binding spheres to ensure they are where the ligand is located

These spheres will be used for initial orientation of the ligand during docking, and provide a rough approximation of the negative space of the receptor.

003: Grid/box

Generating box and grid. The box and grid generation specify the 3-D space where the docking simulation will take place. The box defines the 3-D space where the docking algorithm will search for binding orientations and conformations of the ligand. The box size should be large enough to include the binding space, but not too large to conserve computational cost. The grid pattern allows for energy calculations between protein and ligand. A smaller grid step would allow for more precise calculations but would be computationally expensive and time consuming. A larger grid step would be computationally cheaper but would be lower in accuracy.

Generating the Box

Move to your ~/tutorial/003_gridbox directory. Create an input file for generating a box around the ligand binding site.

vi showbox.in

Insert the following code into the file. These are parameters for the showbox program:

Y
8.0
../002_spheres/selected_spheres.sph
1
1O86.box.pdb

This will construct a box that will enclose the binding spheres that are localized on the binding side. The box will have dimensions of 8.0 Angstroms from the binding spheres.

Run the input file using the following command:

 showbox < showbox.in

An output file titled 1O86.box.pdb will be generated in your local directory.

Generating the Grid

vi grid.in

Insert the following into your input file:

allow_non_integral_charges                no
compute_grids                             yes
grid_spacing                              0.4
output_molecule                           no
contact_score                             no
energy_score                              yes
energy_cutoff_distance                    9999
atom_model                                a
attractive_exponent                       6
repulsive_exponent                        9
distance_dielectric                       yes
dielectric_factor                         4
bump_filter                               yes
bump_overlap                              0.75
receptor_file                             ../001_structure/1O86_protein_nH_ncH.mol2
box_file                                  1O86.box.pdb
vdw_definition_file                       /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
score_grid_prefix                         grid

If grid fails because it cannot find the .defn file, you may need to edit the path of the vdw_definition_file parameter to point to a VDW defn file that actually exists. It should be in the parameters folder of your DOCK6 installation.

Save the file and run using the following command:

 grid -i grid.in -o 1O86_gridinfo.out

An output file with your Grid generation will appear in your directory.

004: Minimization

Before moving toward preforming docking of any fragments/ligands onto your receptor of interest it is important that your original ligand is energy-minimized. This is important before dock is able to calculate any energy interactions between atoms on the rector and ligand.

Move to your ~/tutorial/004_energy_min directory and create an input file using:

vi min.in

In this input file, use the following parameters to minimize the ligand without re-orienting it:

conformer_search_type                                        rigid
use_internal_energy                                          yes 
internal_energy_rep_exp                                      12  
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../001_structure/1O86_ligand_wH_wcH.mol2
limit_max_ligands                                            no  
skip_molecule                                                no  
read_mol_solvation                                           no  
calculate_rmsd                                               yes 
use_rmsd_reference_mol                                       yes 
rmsd_reference_filename                                      ../001_structure/1O86_ligand_wH_wcH.mol2
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 
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  
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_drive.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
ligand_outfile_prefix                                        1O86_min
write_mol_solvation                                          no  
write_orientations                                           no  
num_scored_conformers                                        1   
score_threshold                                              100.0
rank_ligands                                                 no

Finally, run the minimization using DOCK6 as such:

dock6 -i min.in -o min.out

The program should run relatively quickly and create a new Mol2 file called 1O86_min_ranked.mol2. Download this file to your local machine and open it in Chimera along with the original 1O86_ligand_wH_wcH.mol2 to compare the pre- and post-minimized poses. There should be minimal difference between them.

(note that in the above image hydrogens have been hidden for simplicity; the generated Mol2 file and the original ligand file should both be versions where hydrogens are present)

005: Rigid Docking

Rigid docking allows the ligand to be treated as a rigid molecule (no confirmational changes) and determines best orientation for molecule to fit directly into the receptor site.

Move to your ~/tutorial/005_rigid_dock directory and create an input file using the following command:

vi rigid.in

Add the following parameters:

conformer_search_type                                        rigid
use_internal_energy                                          yes 
internal_energy_rep_exp                                      12  
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../004_energy_min/1O86_min_scored.mol2
limit_max_ligands                                            no  
skip_molecule                                                no  
read_mol_solvation                                           no  
calculate_rmsd                                               yes 
use_rmsd_reference_mol                                       yes 
rmsd_reference_filename                                      ../004_energy_min/1O86_min_scored.mol2
use_database_filter                                          no  
orient_ligand                                                yes 
automated_matching                                           yes 
receptor_site_file                                           ../002_spheres/selected_spheres.sph
max_orientations                                             1000
critical_points                                              no  
chemical_matching                                            no  
use_ligand_spheres                                           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
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
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
ligand_outfile_prefix                                        1O86_rigid
write_mol_solvation                                          no
write_orientations                                           no
num_scored_conformers                                        100
write_conformations                                          no
cluster_conformations                                        yes
cluster_rmsd_threshold                                       2.0
score_threshold                                              100.0
rank_ligands                                                 no

Run using the following command:

dock6 -i rigid.in -o rigid.out

The job should take no longer than a minute.

Or run using the following slurm script:

#!/bin/bash
#SBATCH --job-name=1O86_rigid           # Name of the job
#SBATCH --output=rigid.txt  # Standard output file
#SBATCH --error=1O86_error.txt    # Standard error file
#SBATCH --ntasks-per-node=1        # Number of tasks (adjust as needed)
#SBATCH --mail-user=vanie.seecharan@stonybrook.edu          # user
#SBATCH --nodes=1                   # nodes
#SBATCH --time=4:00:00            # Maximum walltime (adjust as needed)
#SBATCH --partition=short-40core    # Correct partition name
# Ensure the input file exists before running the program
if [ ! -f grid.in ]; then
   echo "Error: grid.in file not found!"
   exit 1
fi
# Run the program
/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i rigid.in -o rigid.out 10.0

The following output files will be produced in your directory:

1O86_rigid_scored.mol2
rigid.out

Download the Mol2 file to your computer. This Mol2 file will contain an ensemble of poses which will be messy to visualize all at once. As such, you should use Chimera's ViewDock functionality to view the rigid docked poses. Use Tools >> Surface/Binding Analysis >> ViewDock and open the 1O86_rigid_scored.mol2 file that was created in the docking. The file will be of type DOCK 4, 5, or 6. A separate dialogue box will open that will allow you to select which pose you would like to view.

006: Flexible Docking

Flexible docking accounts for the conformational flexibility of the ligand by sampling the torsions present in it.

Navigate to your ~/tutorial/006_flex_dock and create an input file using the following command:

vi flex.in

Add the following script:

conformer_search_type                                        flex
write_fragment_libraries                                     no
user_specified_anchor                                        no
limit_max_anchors                                            no
min_anchor_size                                              5
pruning_use_clustering                                       yes
pruning_max_orients                                          1000
pruning_clustering_cutoff                                    100
pruning_orient_score_cutoff                                  1000.0
pruning_conformer_score_cutoff                               100.0
pruning_conformer_score_scaling_factor                       1.0
use_clash_overlap                                            no
write_growth_tree                                            no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../004_dock/1o86_lig_min_scored.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       yes
rmsd_reference_filename                                      ../004_dock/1o86_lig_min_scored.mol2
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../002_surface_spheres/selected_spheres.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           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_grid/grid
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
minimize_flexible_growth_ramp                                yes
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_initial_score_coverge                                5
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
ligand_outfile_prefix                                        flex.out
write_mol_solvation                                          no
write_orientations                                           no
num_scored_conformers                                        1
score_threshold                                              100.0
rank_ligands                                                 no

Now, you can run the above file, flex.in, by creating a shell script (flex.sh) as stated below. This will be helpful to have if you need to re-run the job for any reason; rather than re-typing the full dock command, you can save it in the shell script file and run that script instead.

#!/bin/bash

dock6 -i flex.in -o flex.out

Now run the script-

bash flex.sh

DOCK6 program should finish running in a few minutes and should generate the following two files- a) flex.out b) flex_scored.mol2

Now we can transfer the docked files to our local system and visualize the results in chimera.

The docked ligand (colored in cyan) shows good structural overlap with the reference structure (purple). One way of confirming this is by looking at the RMSD value (below) which is below 1 A for this case.

We can also overlay the structures from the three docking types and compare with the reference to observe the best binding pose. The ligand structure obtained due to rigid docking (green) gives the lowest RMSD score of 0.59. Next best RMSD score is obtained from flexible docking (cyan) and then from fixed anchor docking (orange), giving an RMSD of 1.27.

007: Footprint Scoring

Footprint analysis maps out the interaction landscape between a ligand and its target protein. By breaking down the energetics of binding into electrostatic and van der Waals (VDW) contributions, it provides a detailed visualization of how different parts of a ligand interact with specific regions of the protein.

Move to your <~/tutorial/007_footprint</code> directory and create an input file (fps.in).

vi fps.in

Add the following-

conformer_search_type                                        rigid
use_internal_energy                                          no
ligand_atom_file                                             ../004_dock/1O86_min_scored.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
grid_score_primary                                           no
gist_score_primary                                           no
multigrid_score_primary                                      no
dock3.5_score_primary                                        no
continuous_score_primary                                     no
footprint_similarity_score_primary                           yes
fps_score_use_footprint_reference_mol2                       yes
fps_score_footprint_reference_mol2_filename                  ../001_structure/1O86_ligand_wH_wcH.mol2
fps_score_foot_compare_type                                  Euclidean
fps_score_normalize_foot                                     no
fps_score_foot_comp_all_residue                              yes
fps_score_receptor_filename                                  ../001_structure/1O86_protein_wH_wcH.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
minimize_ligand                                              no
simplex_final_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
ligand_outfile_prefix                                        fps
write_mol_solvation                                          no
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
score_threshold                                              100.0
rank_ligands                                                 no

Now create a bash script to run the above create file-

vi fps.sh

#!/bin/bash

echo "Running DOCK for footprint generation..."

dock6 -i fps.in -o fps.out >&fps.log1

echo "Generating plot..."

python /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py fps_footprint_scored.txt  50 >&fps.log2

echo "Done"

As shown above, the .sh script also includes the path to a python file that generates and saves the footprint analysis results as a PDF. Once the script has been executed, transfer the generated PDF to your local system to review the results. The output should resemble the example shown below, showing a visual representation of the electrostatic and van der Waals interactions between the ligand and the protein.

008: 5K Virtual Screening

In this section, you will conduct a virtual screening on a set of druglike potential leads against the 1O86 receptor. Virtual screening of large ligand libraries is one of the main uses of DOCK and other molecular docking suites in drug discovery, as it allows for lead compound identification at much lower cost than traditional in vitro assays.

Input File

Because this section generates a high volume of molecule poses, you may need to make use of your scratch directory on Seawulf. While your home directory has a maximum storage volume of 20 gigabytes, scratch has a storage volume of 20 TERAbytes, so it will easily accommodate the output of your virtual screen. Your scratch directory should be located at /gpfs/scratch/yourusername/. Move there and create a directory for your virtual screening.

Copy the input file from your 006_flex_dock directory into your present directory. We can re-use the majority of input from this file because the docking process is the same in both cases; the only difference is in the number of molecules to be docked. If you like, you can re-name the input file using mv to something like flex_vs.in for clarity.

The only parameter that needs to be changed in the input file is the ligand_atom_file parameter. Instead of the single 1O86_min_scored.mol2, we want to dock a Mol2 file that contains multiple potential drug candidates. You should be able to find several such Mol2 files in /gpfs/projects/AMS536/zzz.programs/VS_libraries/. For this tutorial, we will screen the 5,000 molecule library (VS_library_5K.mol2), but you can elect to do the 100- (or 25,000) molecule library by simply changing the input file name. Just copy the path to the file (should be /gpfs/projects/AMS536/zzz.programs/VS_libraries/VS_library_5K.mol2), open the .in file, delete the current value for ligand_atom_file, and paste in the path. If you don't want to deal with the long filepath, you can also copy the VS_library file to your working directory, and just have the filename as the parameter instead. It is probably also advisable to change the names of other output files in the .in file so that the output is distinguishable from the previous flexible docking.

Note that if you have moved to your scratch directory and used relative paths in the .in file for the receptor sphere file, gridbox, et cetera, those will also need to be changed to reflect your new location. Absolute paths will likely be the most efficient solution for this.

Slurm and Job Submission

Up until this point, you have probably been running dock6 on the head node of Seawulf. This is fine for short, low-intensity jobs, like docking a single molecule or (debatably) generating a grid. However, the head node caters to all users currently accessing Seawulf, and has limited computing power at its disposal. As such, attempting to run a longer job (such as a 5,000 molecule screen) will fully consume the head node's limited resources, slowing down all user sessions in the process until the Seawulf admins notice and kick you. To safely utilize the full computing power of Seawulf, you need to submit a job to one of its allocated high-power computing nodes using its queueing system. This system tracks all jobs that have been submitted by various users and allocates them to processors as they are freed up, maximizing the productivity and efficiency of the computing cluster while ensuring a smooth user experience. The system Seawulf uses for this queue tracking is called Slurm (Simple Linux Utility and Resource Management).

Slurm is implemented as a module on Seawulf, and needs to be loaded into your environment before it can be used. You can load it by typing module load slurm into your terminal from any directory. Of note, you will need to do this every time you start a new SSH session. If you want the module to always be loaded when you log in, you can add the command to your .bashrc file (see section 000 for instructions on how to modify your .bashrc).

Once the module has loaded, you can use the command sinfo to view what processors are present on Seawulf. If you are on Milan, you should see 40- and 96-core queues of varying lengths (short, medium, long), as well as some specialized GPU cores and high memory cores. The Seawulf website has some good descriptions of what cores are available and the duration of jobs allowed on them. sinfo --state=idle allows you to see what queues have cores idle; this is helpful for knowing where a job can start running immediately.

To submit a job to a queue, you need to create a special job script file that will tell the queue everything it needs to know about the job, as well as what commands to run. Here is what that file will look like for our VS run:

#!/bin/bash
#
#SBATCH --job-name=1o86_vs
#SBATCH --output=vs_output.txt
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=96
#SBATCH --time=48:00:00
#SBATCH -p long-96core

module load intel/mpi/64/2018/18.0.3

mpirun -np 96 dock6.mpi -i flex_vs.in -o flex_vs.out

A line-by-line breakdown of this file:

#!/bin/bash is called a shebang, and is used in unix shell scripts to indicate that bash should be used to interpret and execute the script.
#SBATCH --job-name=1O86_vs tells slurm what our job is called; this can be changed to whatever strikes your fancy without consequence
#SBATCH --output=vs_output.txt tells slurm where to output information about the job itself. If jobs are not running properly, check this file for errors.
#SBATCH --nodes=1 tells slurm how many computing nodes we want for this job. 1 is appropriate here because we are not using any parallel processing functionality.
#SBATCH --ntasks-per-node=96 tells slurm how many tasks it should expect to run per node. There are no strict guidelines on this, but setting it equal to the number of cores in the node (96 or 40 on Milan) is a good default.
#SBATCH --time=48:00:00 tells slurm the maximum amount of time it should allocate for this job. The best thing to do here is request the maximum time possible for the queue; check the Seawulf website for each queue's parameters. Here, because we are submitting to the long-96core queue, we are requesting the queue maximum of 48 hours; our job will likely not take that long.
#SBATCH -p long-96core tells slurm which queue we would like to submit to; in this case, we are submitting to the long-term 96-core queue.
module load intel/mpi/64/2018/18.0.3 loads a module that allows for parallel processing, greatly speeding up job progress.
mpirun -np 96 dock6.mpi -i flex_vs.in -o flex_vs.out is the actual command we would like to run in the job. This particular command asks mpirun, which implements parallel processing, to run the MPI version of dock6 for our screening. The np parameter provides information on the number of processors available for MPI; this can be calculated by multiplying nodes by ntasks-per-node (96 * 1 in this case).

Now that you have a sense of what we're trying to do, create a shell file with a recognizable name (ex, job.sh) and either copy-paste or re-type the above input into the file, making any modifications to the dock path or input filename as needed. Save and exit the file.

Finally, you are ready to submit your first job to the queue. Use the command sbatch job.sh to submit your job file. If slurm accepts it, you will be provided a job number.

You can use the command squeue -u yourusername to check the status of your job. If you do not see it in the queue directly after submitting, it has likely encountered an error, and you will need to troubleshoot. A good place to start will be reading any generated output files.

Otherwise, it will likely start as PD (pending) for a time (depending on how full the queue is, this can vary from a minute to a day. Sorry.) before switching to R (running). As it runs, you should see .mol2 files spontaneously created in the directory. Make sure to check semi-regularly that the job is still running.

Once the virtual screen has finished, you should have a .mol2 file in your directory that contains the best poses of the 5,000 ligands that were screened, according to purely grid-based docking.

Re-scoring Docked Molecules

Although grid scoring provides a good initial look at the most favorable poses of the given molecules, it is generally a good idea to re-score the poses provided by a different criteria to determine a final order. In this case, we will use footprint similarity scoring (FPS) as our re-scoring function. Once again, we can copy the input file that we used in the single-molecule footprint scoring example, and change the ligand_atom_file parameter from the 1O86 ligand to the output poses from the virtual screening. You should also change ranked_ligands to yes (towards the end of the file), and add a line with the parameter max_ranked_ligands set to 500 at the end of the file. This will ensure that the final .mol2 is a manageable size, while retaining the best poses of the docking. Finally, set the ligand_outfile_prefix parameter to something that will distinguish it from the other output already in the directory. Write and exit the file, and rename it to something appropriate like rescore.in.

Because this re-scoring uses rigid docking and no grid calculations, it should be relatively lightweight and safe to run on the head node. If you want to be safe (or if it is still running after a couple minutes), you can cancel it and use the command srun -p short-96core -t 1:00:00 --pty bash to instead open up an interactive bash session on one of the computing nodes. This will let you use an interactive terminal in a manner identical to the head node, but direct all processing requests to an available computing node instead of using the head node's resources. Unfortunately, it is also subject to the whims of the queue availability, so you may have to wait a while or time strategically to obtain an available node.

Once you run the re-scoring using dock6 -i rescore.in -o rescore.out, you should see a re-scored ligand file in the directory with the prefix indicated in the rescore.in file. If you want, you can copy this .mol2 file to your home directory so that it is not purged after 30 days (a convenient feature of the scratch directory). After that, download it to your local machine using scp.

Viewing VS Results in Chimera

Thanks to our infallible foresight, we have saved only the 500 best ligands to visualize in Chimera, as opposed to the original, crash-inducing number of 5,000. To analyze the poses of these ligands, launch Chimera and File >> Open your receptor .mol2 file. Then, navigate to Tools >> Surface/Binding Analysis >> ViewDock, and open the 500-ligand .mol2 file that you have just downloaded. Chimera may lag for a minute depending on your system specs, but should eventually provide a dialogue box and display one ligand in (hopefully) your receptor's binding site.

The dialogue box allows you to select one or multiple ligands at a time to view, and displays their scores in a nice table format. You can view additional columns of data in the dialogue box by navigating to Column >> Show and selecting the desired parameter, and view multiple ligands at a time by clicking one, then holding shift and clicking another.

Congratulations! You have successfully conducted a virtual screening, learned how to use slurm in the process, and now have results for potential lead compounds targeting this receptor.

009: Genetic Algorithm

In addition to providing a platform for traditional virtual screening methods, DOCK also implements several unique algorithms for de novo-type drug design. One of these is the genetic algorithm (GA), which accepts one or several "parent" molecules and "mutates" them with basic substitutions, insertions, or deletions using a standard molecular fragment library before culling the resultant "population" based on user-specified metrics. The intent is to iteratively improve molecules over several "generations" of mutation-cull steps so that new chemical space can be explored, and more potent ligands found.

In order for the GA to mutate the provided parent molecules, it needs a standard library of molecular fragments to draw from. DOCK provides a foundational library that is generally effective in most GA applications, but can also accept .mol2 files to fragment and use as a custom library. To make this tutorial as educational as possible, you will learn how to fragment a molecule and add it to the foundational fragment library before running the genetic algorithm.

First, move to your 009_gen_alg directory and create a directory within it called fraglib/. Then, move into that directory in preparation for creating the fraglib generation input file.

Generating Fragments

The overall goal in this section is to use DOCK to fragment the ligand present in the 1O86 system, and add those fragments to the foundational library. The backbone of this operation is the write_fragment_libraries option in the DOCK input file. Below is what a sample input file would look like; you may copy and paste it directly, but we recommend moving through DOCK's decision tree and understanding what defaults the program has that we are changing. In this instance, we override several defaults such as orient_ligand and score_molecule, as these are unnecessary for the pure operation of generating ligand fragments. We will refer to the input file as fraglib_gen.in Some parameters are left as exercises to the reader; refer back to previous steps if confused.

conformer_search_type                                    	flex
write_fragment_libraries                                 	yes
fragment_library_prefix                                  	1O86_lig_fraglib
fragment_library_freq_cutoff                             	1
fragment_library_sort_method                             	freq
fragment_library_trans_origin                            	no
use_internal_energy                                      	no
ligand_atom_file                                         	FILL IN 1O86 LIGAND MOL2
limit_max_ligands                                        	no
skip_molecule                                            	no
read_mol_solvation                                       	no
calculate_rmsd                                           	no
use_database_filter                                      	no
orient_ligand                                            	no
bump_filter                                              	no
score_molecules                                          	no
atom_model                                               	all
vdw_defn_file                                            	FILL IN VDW.DEFN FILEPATH
flex_defn_file                                           	FILL IN FLEX.DEFN FILEPATH
flex_drive_file                                          	FILL IN FLEX_DRIVE FILEPATH
ligand_outfile_prefix                                    	1o86_fraglib
write_mol_solvation                                      	no
write_orientations                                       	no
num_scored_conformers                                    	1
score_threshold                                          	100.0
rank_ligands                                             	no

Once you have created this input file and inserted the relevant filepaths, you can run DOCK to generate the fragments:

dock6 -i fraglib_gen.in -o fraglib_gen.out

Because we are only fragmenting one molecule, this program should be fine to run on the head node, and should finish in a couple seconds. Once it finishes, you should see present in the directory:

Four .mol2 files containing "linker", "rigid", "scaffold", and "sidechain" in their names; will be referred to as 1o86_fraglib_TYPE.mol2
A file ending in "torenv.dat" (referred to as 1o86_lig_torenv.dat hereafter)
An output_scored.mol2 file
A .out file with whatever name you specified

The set of four .mol2 files contain all the fragments that DOCK was able to generate from the original molecule, and the *torenv.dat file is a record of all the torsion-able bonds that DOCK cleaved to generate the fragments.

Combining Fragment Libraries

Now that we have generated fragments and associated torsions from our ligand, we need to combine them with the standard DOCK fragment library and associated torsion environments. The torsion environment combination can be accomplished via a python script.

First, determine the path to the default DOCK torsion environment collection. It should be located in the parameters folder associated with your DOCK installation. At the time of writing, the full path is /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_torenv.dat

Next, determine the path for the python script used to combine torsion environments. It should be in the same bin directory as your dock6 command. At the time of writing, there is an instance at /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/combine_torenv.py

Once you have found paths that work for both of these files, you can combine the standard torsion environment with the newly generated custom one by running

python insert_path_here/combine_torenv.py ./1o86_lig_torenv.dat insert_path_here/fraglib_torenv.dat

(note that you may need to use the command module load python if you encounter a python-related error in running this) Once the script finishes, you should have a full_fraglib.dat, full_sorted_fraglib.dat and unique_full_sorted_fraglib.dat files in your directory. We will be using the "unique" variant for our genetic algorithm process.

We also need to combine the .mol2 files that we have generated from our ligand with the standard DOCK-provided ones. Because .mol2 files just contain lists of molecules without any special header/footer text, they can just be concatenated together by a shell script. Combine the linker, scaffold, and sidechain .mol2 files with their counterparts in the parameters/ folder using cat; an example would be:

cat insert_path_here/parameters/fraglib_linker.mol2 ./1o86_fraglib_linker.mol2 >> combined_fraglib_linker.mol2

(Note that we do not do anything with the "rigid" .mol2; this set of fragments is not needed to run the GA). After you do this process for all three variants of the fraglib .mol2s, you will be ready to run the genetic algorithm. It may be advisable to move the ligand-specific fragment library mol2s to a sub-directory in order to prevent cluttering/confusion.

Running the GA

With all preparation completed, we can now start optimizing molecules using the genetic algorithm. We will use our original ligand as the "parent" molecule for the first generation, and allow the algorithm to mutate it into new molecules for fifty generations.

Aside from the filepaths/filenames for the various fraglibs, ligand, protein spheres, and .defn files, the only parameters we are changing from default in the .in file are ga_max_generations and ga_mutate_parents. Maximum generations are lowered to 50 for computational tractability, and parents must be mutable because we only have one molecule to start with; the population would grow very slowly or even die off if we did not allow parental recombination. A full sample input file is given below (but as always, do please try to do it yourself):

conformer_search_type                                    	genetic
ga_molecule_file                                         	ORIGINAL 1O86 LIGAND MOL2
ga_utilities                                             	no
ga_fraglib_scaffold_file                                 	FRAGLIB_SCAFFOLD MOL2
ga_fraglib_linker_file                                   	FRAGLIB_LINKER MOL2
ga_fraglib_sidechain_file                                	FRAGLIB_SIDECHAIN MOL2
ga_torenv_table                                          	FRAGLIB TORENV DAT
ga_max_generations                                       	50
ga_xover_on                                              	yes
ga_xover_sampling_method_rand                            	yes
ga_xover_max                                             	150
ga_bond_tolerance                                        	0.5
ga_angle_cutoff                                          	0.14
ga_check_overlap                                         	no
ga_mutate_addition                                       	yes
ga_mutate_deletion                                       	yes
ga_mutate_substitution                                   	yes
ga_mutate_replacement                                    	yes
ga_mutate_parents                                        	yes
ga_pmut_rate                                             	0.3
ga_omut_rate                                             	0.7
ga_max_mut_cycles                                        	5
ga_mut_sampling_method                                   	rand
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
ga_selection_method                                      	elitism
ga_elitism_combined                                      	yes
ga_elitism_option                                        	max
ga_max_num_gen_with_no_crossover                         	25
ga_name_identifier                                       	1o86_ga
ga_output_prefix                                         	1086_ga_out
use_internal_energy                                      	yes
internal_energy_rep_exp                                  	12
internal_energy_cutoff                                   	100.0
use_database_filter                                      	no
orient_ligand                                            	yes
automated_matching                                       	yes
receptor_site_file                                       	RECEPTOR SPHERES .SPH
max_orientations                                         	1000
critical_points                                          	no
chemical_matching                                        	no
use_ligand_spheres                                       	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                                   	GRID PATH
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                                            	VDW DEFN FILE
flex_defn_file                                           	FLEX DEFN FILE
flex_drive_file                                          	FLEX_DRIVE FILE

We will also need to create a batch file to run the GA using slurm, as it is an intensive process that will take a number of hours to run. A sample is provided below; you should adopt yours to the appropriate queue, job name, time to run, DOCK path, and input filename:

#!/bin/bash
#
#SBATCH --job-name=1o86_GA
#SBATCH --output=ga_output.txt
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#SBATCH --time=4:00:00
#SBATCH -p short-40core

change_this_to_your_path_to_dock/bin/dock6 -i genalg.in -o genalg.out

Use sbatch job.sh to submit this per usual, and check up on it regularly. The first few generations should go relatively quickly, with a slowdown as the molecular population increases past generation 8-10. If you want to track the population growth, you can use grep -c "Name" *mol2 to view the molecule populations of every .mol2 file that has been written so far.

Analysis

Once the genetic algorithm has finished running, you can view the final generation's best molecules and poses in Chimera via the same process outlined in section 008. To review, this will entail downloading the final .mol2 to your local machine (generation 50 in this case), launching Chimera, opening the receptor .mol2 via File >> Open, and using the Tools >> Structure/Binding Analysis >> ViewDock tool to load the ligand .mol2 file in a conveniently viewable format. An example of this can be seen below:

010: De Novo Design Example

De Novo Design

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.

In this tutorial, you will be guided through a Denovo refinement calculation. This kind of calculation involves deleting a part of a ligand, creating a dummy atom, and using the De Novo design algorithm to 'regrow' that part of the ligand based on user defined parameters. The way in which the 'regrow' process happens comes from the algorithm pulling molecules from fragment libraries that contain scaffolds, linkers, and sidechains. The user defined parameters will dictate which libraries the algorithm can pull from.

The outcome will be a series of refinements that will retain a desired interaction in 1O86.

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_protein_wH_wcH.mol2 file, then your 1O86_ligand_wH_wcH.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 >> Show Next, navigate to Select >> Invert(selected models), here you'll notice most of the protein is highlighted Lastly, Return to Actions >> Atoms/Bonds >> 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_wH_wcH.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 or a text editor and change the atom type of C9 to Du:

First in the terminal, type the command

  vi 1O86_ligand_Du.mol2

Or, open the Mol2 file in your text editor of choice.

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 C9 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 yourusername@login.seawulf.stonybrook.edu:'/gpfs/home/yourusername/tutorial/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

  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                                             DN.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

Once you've filled out the input file, you can then go ahead and run the calculation

  dock6 -i DN.in -o DN.out

After running the calculations, the following output files will be generated:

 DN.out
 DN.out.anchor_1.root_layer_1.mol
 DN.out.completed.denovo_build.mol2
 DN.out.denovo_build.mol2

Examining the output file you can see how many molecules were grown.

In this case there are 21 different attached molecules.

Now, copy over the DN.out.completed.denovo_build.mol2 to your home computer

   scp yourusername@login.seawulf.stonybrook.edu:'/gpfs/home/yourusername/tutorial/010_de_novo/DN.out.completed.denovo_build.mol2' .

Visualizing the Molecules in Chimera

Head over to Chimera and go to Tools >> Surface/Binding Analysis >> Scroll down to where you see ViewDock and select it

Then select the DN.out.completed_denovo.mol2

The following menu will appear:

You can navigate through the list of molecules that were grown from the calculations.

You'll notice that the best scoring ligand retained the oxygens from the original ligand:

Opening the original ligand mol2, you'll see that the molecules are almost identical

If you return to the ViewDock menu and highlight all of the ligands. You will be able to see a depiction of all of the different refinements.

This can be done by going to Tools >> ViewDock >> Raise Now that the menu has been prompted hold down your shift key and select the first ligand, then scroll down and select the last ligand. All your molecules will be shown overlapping on Chimera:

Well done, you've now completed a simple denovo calculation!

Running a Generic De Novo Calculation

In this part of the tutorial, you will be running a generic denovo calculation. What this means is that you take an anchor, or don't specify one, and grow a ligand around parts of the molecule. These parts of the molecule are dictated by the selected spheres that were calculated in the second part of the VS tutorial. The end result becomes a series of newly 'grown' ligands based on the user defined parameters. These parameters are what will bias the denovo growth to meet a certain criterian (i.e. a specific molecular weight). For this tutorial, you will select an anchor and use that to grow a series of ligands, which you will then be able to see on chimera.

To start, lets create a new directory in your 010_de_novo directory. Lets call it generic.

   mkdir generic

Selecting an Anchor

Now that you have a working directory for this calculation, lets go ahead and create an anchor

file to run the generic denovo calculation. For our anchor of choice, we will use the most popular

sidechain from dock6's current library. To start off, copy the library mol2 file to your home directory from

seawulf:

    scp yourusername@milan.seawulf.stonybrook.edu:'/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2' .

It's a pretty hefty file and the way you are going to open the file is by using ViewDock on Chimera.

Navigate to Chimera and select Tools --> Surface/Binding Analysis --> View Dock

Select the fraglib_sidechain.mol2 file.

On chimera you'll see a methyl-ethyl sidechain popup and the View Dock menu to toggle through other sidechains:

As mentioned before, you are going to use the most popular sidechain as the anchor for this calculation.

On the View Dock Menu go to Column --> Show --> FREQ

This is the frequency in which these particular sidechains occur in the dock6 testset:

Ironically, the methy ethyl sidechain appears to be the most popular sidechain. This will be the anchor of choice.

Go to File --> Save Mol2

Lets call it Anchor.mol2

Additionally, make sure that only the first model is selected in the Select Model panel like so:

Select Save. You can also verify that there is only one sidechain in the mol2 by viewing it on the terminal

  vi Anchor.mol2

The file should look like this:

Now you can go ahead and copy this file over to the generic directory in seawulf

 scp Anchor.mol2 yourusername@milan.stonybrook.edu:'/gpfs/yourusername/tutorial/010_de_novo_/generic'

Running the Calculations

Now that you're on seawulf in the generic directory with your Anchor.mol2 file,

lets create the necessary files to run the generic denovo calculation.

First, create an input file, lets call it GDN.in.

Just like when running the refinement calculation, you are encouraged to create an empty input file and follow the dock6 question tree.

To create an empty input file run the following command:

    touch GDN.in

Then, use dock6 to initiate the question tree:

    dock6 -i GDN.in

Use the following sample input file as a template when navigating the question tree:

  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                                       ../generic/Anchor.mol2
  dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_torenv.dat
  dn_name_identifier                                           generic
  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                                   550.0
  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
  dn_write_prune_dump                                          no
  dn_write_orients                                             no
  dn_write_growth_trees                                        no
  dn_output_prefix                                             generic
  use_internal_energy                                          yes
  internal_energy_rep_exp                                      12
  internal_energy_cutoff                                       100.0
  use_database_filter                                          no
  orient_ligand                                                yes
  automated_matching                                           yes
  receptor_site_file                                           ../002_spheres/selected_spheres.sph
  max_orientations                                             1000
  critical_points                                              no
  chemical_matching                                            no
  use_ligand_spheres                                           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_de_novo.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

After creating the input file, you will need to create a slurm input file to run this calculation.

 vi gdn.slurm

Type the following into the slurm file:

 #!/bin/bash
 #
 #SBATCH --job-name=1O86_generic_de_novo
 #SBATCH --output=generic_dn_output.txt
 #SBATCH --ntasks-per-node=24
 #SBATCH --nodes=4
 #SBATCH --time=4:00:00
 #SBATCH -p short-96core

 dock6 -i GDN.in -o GDN.out

To run the calculation submit a job with the slurm file:

   sbatch gdn.slurm

The job itself may take awhile to finish. It is highly recommended that you check to see if your job is still running and that your .out file to see if there are any errors.

After the calculations have run, the following files will show up in your directory:

 GDN.out                             generic_dn_output.txt
 generic.anchor_1.root_layer_1.mol2  generic.anchor_1.root_layer_5.mol2      
 generic.anchor_1.root_layer_2.mol2  generic.anchor_1.root_layer_6.mol2
 generic.anchor_1.root_layer_3.mol2  generic.anchor_1.root_layer_7.mol2
 generic.anchor_1.root_layer_4.mol2  generic.completed.denovo_build.mol2
                                     generic.denovo_build.mol2

These illustrate the different layers of growth that were specified in the input file, the generic.completed.denovo_build.mol2 contains all of the finished molecules regardless of how many layers of growth. To view how many molecules are in this output file, type the following line in your terminal:

  grep -c "SMALL" generic.completed.denovo_build.mol2

You'll notice that the number of molecules in this file come out to be 2350. That's okay, go ahead and transfer this file onto your home computer:

   scp yourusername@milan.stonybrook.edu:'gpfs/yourusername/tutorial/010_de_novo/generic/generic.completed.denovo_build.mol2' .

Visualizing The Results

To view the molecules that were grown, use the View Dock tool in Chimera. The procedure is the same as when you were selecting an anchor. You should wait about 30 seconds as there are a large chunk of molecules being loaded into chimera. Once Chimera is finished loading you will see an image of a finished sidechain and the View Dock Menu:

You want to view the sidechains that have better overall grid scores. On the View Dock menu, go to Column --> Show --> Grid_Score. You'll see that the Grid_Score column is columned. Let's sort the Grid_Score column in descending order(i.e. from greatest to least). To do this, click on the Grid_Score title, you'll notice that there's now an arrow head over the column. Keep clicking on the column until you see that the arrow head is pointing up:

Now the best scoring molecule that was grown is at the top of the list and here's what it looks like:

Load in the 1O86_fixed_protein.pdb and the 1O86_ligand_nH_ncH.mol2 . On Chimera, select Actions --> Ribbon --> hide. This will give a clear picture of the ligand having slight overlap with the grown ligand in the protein:

Congratulations, you've successfully run a generic denovo calculation.

@@ Line 1: / Line 1: @@
-== DOCK Tutorial using PDB 1O86 ==
+==  DOCK Tutorial using PDB 1O86 ==
-[intro text]
+This tutorial is a series of modules designed to familiarize a new user with the basic functions and features of DOCK6, as well as provide guidance on its execution and analysis of results. Modules should be read in a linear fashion, as each module builds on the prior one.
+The [https://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm the full DOCK manual] contains much more information than this tutorial, and as such is recommended as a resource if the information provided herein proves unsatisfactory.
 == 000: Foundations ==
@@ Line 12: / Line 14: @@
 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 [https://www.cgl.ucsf.edu/chimera/docindex.html on the official site].
-== 001: Structure Prep ==
+[[File:ChimeraMenu.png]]
-Download PDB, separate lig/rec, model loops, addH/charge
-'''Downloading the PDB'''
+More extensive documentation on Chimera and its functions is available [https://www.cgl.ucsf.edu/chimera/docindex.html on the official site].
-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:
-[[File:1O86_RCSB_1.png]]
-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:
-[[File:1O86_RCSB_2.png]]
-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'''
-. Open 1O86 protein only file in chimera and hit select > show> surface
-. Write the DMS file by choosing tools>structure editing>Write DMS
-. Upload the DMS file to your directory
-. Create a sphere input file using the following command:
- vi INSPH
-. Paste the following into your input file:
- ./IO86.dms
- R
- X
-.0
-.0
-.4
- IO86.sph
-. Run the program with the following command
- sphgen -i INSPH -o OUTSPH
-. 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 [https://en.wikipedia.org/wiki/Lipinski%27s_rule_of_five 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:
-[[File:Ligand_In_1O86_DN.png]]
-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:
-[[File:1O86_Zone.png]]
-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:
-[[File:highlight.png]]
-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
-[[File:Clear_picture.png]]
-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
-<code> vi 1O86_ligand_Du.mol2 </code>
-Find the C9 atom and modify the atom type. Your input file should look like this:
-[[File:Input_file.png]]
-Save it.
-Now lets verify this change by opening the mol2 file on Chimera:
-[[File:New_dummy_Ligand.png]]
-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
-<code> scp 1O86_ligand_Du.mol2 username@login.seawulf.stonybrook.edu:'/gpfs/username/010_de_novo'</code>
-=== Running The Denovo Calculation ===
-In your 010_De_Novo folder create an empty input file:
-<code> touch DN.in </code>
-Then prompt the question tree with the dock program:
-<code> dock6 -i DN.in </code>
-Follow the question tree and use the following sample input file as a template
-Last login: Sat Jan 25 20:39:22 on ttys000
-(base) supremestudier@Evans-MBP ~ % ls
-ay7.cif
-dqx.cif
--sat-results.csv
-ees.cif
-tj3.cif
-fev.cif
-rfw.cif
-A Hardworking Freshman.txt
-A1_Evan.S.ipynb
-A2_EvanS.ipynb
-AbdulA&YelisvetF_FinalProject_TeenBeachMovieQuiz_.ipynb
-An ambitious kid.txt
-Applications
-Assignment3_EvanS.ipynb
-BE.log
-Beer's Law.xlsx
-Biostats
-CYS_waterbox.pdb
-Customer Data2.xlsx
-Cys.log
-Cysteine_waterbox.pdb
-Data_EvanS.ipynb
-Debugging_EvanS.ipynb
-Desktop
-Documents
-Downloads
-Econ160
-EvanS_W12.ipynb
-Evan_Spector_API_Lab#2.ipynb
-Evan_Spector_API_Lab.ipynb
-Evan_Spector_API_LabMiniProject.ipynb
-Evan_Spector_API_LabMockAPI.ipynb
-Evan_Spector_WebScraping_LabDemos.ipynb
-Evan_Spector_WebScraping_MiniProject.ipynb
-Excel_Evan S.ipynb
-Fate.png
-Final Exercise.xlsx
-Final Project.ipynb
-FinalProject_EvanS-2 - Evan H Spector.ipynb
-FinalProject_EvanS.ipynb
-GS_2.png
-G_waterbox.pdb
-Gall Diameter by Site Boxplot.png
-Game.ipynb
-Graph 1 108.xlsx
-Graph 2 108.xlsx
-Graph 3 108.xlsx
-Guest Speaker Walk through.ipynb
-Hello World.ipynb
-High school Senior Checklist.txt
-Invalid Data.xlsx
-Keq Data.xlsx
-Ksp Data.xlsx
-Lab 2_ Evan S..ipynb
-Lab3_EvanS.ipynb
-Lab5_EvanS.ipynb
-Lab_1 Evan S.ipynb
-Lat.png
-Library
-Linear Regression for Dye.xlsx
-Loops_EvanS.ipynb
-Mambaforge-Darwin-x86_64.
-Methyl Red Excel.xlsx
-Movies
-Music
-NBA_players_2015.csv
-Overdue Customers 2.xlsx
-Oxamide_n2_water.agr
-Peer.ipynb
-Pictures
-Practice.ipynb
-Profile Picture.jpg
-Project.ipynb
-Prototype.ipynb
-Prototype_5.ipynb
-Public
-Quiz Review.ipynb
-README.md
-Reaction 1 Data.xlsx
-Reaction 2 Data.xlsx
-Reaction 3 Data.xlsx
-Reaction 4 Data.xlsx
-Red Cross - Wallet Card - Individual_SD-37055011.pdf
-Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf
-Review Lab_ Evan S..ipynb
-Review3_EvanS.ipynb
-Review_2.ipynb
-SAT__College_Board__2010_School_Level_Results.csv
-Sine and Cosine Curve.ipynb
-Split_2.tga
-SpotifyFinalProject.ipynb
-SulfurCys.agr
-TSLA.csv
-UNL.agr
-Untitled Folder
-Untitled.ipynb
-Untitled1.ipynb
-Untitled2.ipynb
-WAT_O.agr
-Working with OpenPyXL.xlsx
-anaconda3
-eclipse
-eclipse-workspace
-final_project_draft4.ipynb
-helloWorld.py
-install.sh
-introdata.ipynb
-java.log.34001
-java.log.37118
-job_skills.csv
-jupyter_mac.command
-matlab_crash_dump.6196-1
-miniconda3
-multiplot.agr
-opt
-plotting-with-pandas.ipynb
-population-by-country-2020.zip
-population_by_country_2020.csv
-rmsd.agr
-source.venv
-test.encrypted
-test.txt
-twitter-workshop-master.zip
-(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Permission denied, please try again.
-ehspector@login.seawulf.stonybrook.edu's password:
-Permission denied, please try again.
-ehspector@login.seawulf.stonybrook.edu's password:
-(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login1 ~]$ home
-(base) [ehspector@login1 espector]$ cd ..
-(base) [ehspector@login1 rizzo]$ cd ..
-(base) [ehspector@login1 projects]$ ls
-ABCD                  EssigGroup            MaoGroup             SchedelGroup
-AllamGroup            FarhadzadehGroup      McDonoughGroup       SeeligerGroup
-AllenGroup            FernandezGroup        McGrewGroup          SehgalGroup
-AMS530                FernandezReuterGroup  McKinnonGroup        ShepsonGroup
-AMS536                FrenkelGroup          MehmoodGroup         SherGroup
-AMS598                FutcherGroup          MelikerGroup         SheridanGroup
-AMS691                GenomicsCore          MihalacheGroup       ShilkrotGroup
-Aponte-RiveraGroup    GergenGroup           MirandaGroup         SiegmannGroup
-ArmitageGroup         glimm                 MitchellGroup        SladeGroup
-AssanisGroup          GoblerGroup           MoellerGroup         SmaersGroup
-BEE690                GoldbartGroup         MofakhamGroup        SOC591
-BenchmarkGroup        HCPGroup              MohantyGroup         SOC595
-BenderGroup           HeinzGroup            MollProject          StanacevicGroup
-BernauerGroup         HollisterGroup        molssi               SternGroup
-BialkowskaGroup       HoltGroup             MoutsanidisGroup     SyritsynGroup
-BIO303                hpc_support           MujicaGroup          TakeuchiGroup
-BluesteinGroup        HudsonGroup           NadkarniGroup        TanGroup
-BurguenoGroup         IACSPDPGroup          NMRPIJodeyGroup      TaylorGroup
-CalderGroup           JiaoGroup             NMRPILipshultzGroup  TeraChemGroup
-CanliGroup            JohnsonGroup          NMRPIMingNgaiGroup   Tesse
-CarlsonGroup          JonesBozarthGroup     NMRPIPicartGroup     TestGroup1
-CascanteBonillaGroup  JonesGroup            OjimaGroup           ThackerGroup
-ChangGroup            JonesSkienaGroup      OkeomaGroup          ThakurGroup
-ChapmanGroup          KarzaiGroup           PadillaGroup         ThorneGroup
-CheCastaldoGroup      KeeGroup              PariseGroup          TitleGroup
-ChenGroup             KeeJiaoGroup          PercivalGroup        TsybychevGroup
-ChenXGroup            KellyGroup            PerlmanGroup         VanSnellenbergGroup
-CheungGroup           KhosronejadGroup      PernaGroup           VaskaGroup
-ChowdhuryGroup        KimGroup              PicartGroup          VeeramahGroup
-ChowdhuryRGroup       KirylukGroup          PiretGroup           VitekGroup
-ColleGroup            KodnerGroup           PolakGroup           VonDerLindenGroup
-CollierGroup          KogaGroup             PoonGroup            VorkasGroup
-CSE416                KozakovGroup          PowersGroup          WangGroup
-CSE504                KritzerGroup          PSY610               WanGroup
-CSE519                KrsticGroup           PSY620               WangXGroup
-CSE590                KrsticQuantumGroup    QuantComp            WeinachtGroup
-CSE628                KurcGroup             RahmeGroup           WeinsteinGroup
-DAndreaGroup          LeungGroup            RajputGroup          WeissmanGroup
-DavalosGroup          LevineGroup           RambowGroup          WilsonGroup
-DeLorenzoGroup        LiGroup               RestGroup            WymoreGroup
-DengYasarGroup        LoverdeGroup          ReuterGroup          YeGroup
-DevarajanGroup        LuGroup               RiosGroup            YouGroup
-DheillyGroup          LuhmannGroup          rizzo                ZhangGroup
-DillGroup             LuoGroup              rjh                  ZhanGroup
-DoboliGroup           LynchGroup            RosatiGroup          ZhangYGroup
-DubnauGroup           MaffeiGroup           samples              ZhaoGroup
-EBH370                MaGroup               SampsonCryoEMGroup   ZhouGroup
-EBH381                MakGroup              SampsonGroup         ZhouMedAdvGroup
-EkblomGroup           MallipattuGroup       SamulyakGroup        ZhuGroup
-(base) [ehspector@login1 projects]$ cd AMS536
-(base) [ehspector@login1 AMS536]$ ls
-  2019  2021  2023  2025            zzz.anchors
-  2020  2022  2024  get_anchors.py  zzz.programs
-(base) [ehspector@login1 AMS536]$ cd 2025
-(base) [ehspector@login1 2025]$ ls
-additional_files
-(base) [ehspector@login1 2025]$ cd additional_files/
-(base) [ehspector@login1 additional_files]$ ls
-sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  touch.sh
-(base) [ehspector@login1 additional_files]$ cd ..
-(base) [ehspector@login1 2025]$ cd ..
-(base) [ehspector@login1 AMS536]$ cd 2025
-(base) [ehspector@login1 2025]$ pwd
-/gpfs/projects/AMS536/2025
-(base) [ehspector@login1 2025]$ vi ~/.bashrc
-(base) [ehspector@login1 2025]$ home
-(base) [ehspector@login1 espector]$ source ~/.bashrc
-(base) [ehspector@login1 espector]$ class
-(base) [ehspector@login1 2025]$ home
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP ~ % ls
-ay7.cif
-dqx.cif
--sat-results.csv
-ees.cif
-tj3.cif
-fev.cif
-rfw.cif
-A Hardworking Freshman.txt
-A1_Evan.S.ipynb
-A2_EvanS.ipynb
-AbdulA&YelisvetF_FinalProject_TeenBeachMovieQuiz_.ipynb
-An ambitious kid.txt
-Applications
-Assignment3_EvanS.ipynb
-BE.log
-Beer's Law.xlsx
-Biostats
-CYS_waterbox.pdb
-Customer Data2.xlsx
-Cys.log
-Cysteine_waterbox.pdb
-Data_EvanS.ipynb
-Debugging_EvanS.ipynb
-Desktop
-Documents
-Downloads
-Econ160
-EvanS_W12.ipynb
-Evan_Spector_API_Lab#2.ipynb
-Evan_Spector_API_Lab.ipynb
-Evan_Spector_API_LabMiniProject.ipynb
-Evan_Spector_API_LabMockAPI.ipynb
-Evan_Spector_WebScraping_LabDemos.ipynb
-Evan_Spector_WebScraping_MiniProject.ipynb
-Excel_Evan S.ipynb
-Fate.png
-Final Exercise.xlsx
-Final Project.ipynb
-FinalProject_EvanS-2 - Evan H Spector.ipynb
-FinalProject_EvanS.ipynb
-GS_2.png
-G_waterbox.pdb
-Gall Diameter by Site Boxplot.png
-Game.ipynb
-Graph 1 108.xlsx
-Graph 2 108.xlsx
-Graph 3 108.xlsx
-Guest Speaker Walk through.ipynb
-Hello World.ipynb
-High school Senior Checklist.txt
-Invalid Data.xlsx
-Keq Data.xlsx
-Ksp Data.xlsx
-Lab 2_ Evan S..ipynb
-Lab3_EvanS.ipynb
-Lab5_EvanS.ipynb
-Lab_1 Evan S.ipynb
-Lat.png
-Library
-Linear Regression for Dye.xlsx
-Loops_EvanS.ipynb
-Mambaforge-Darwin-x86_64.
-Methyl Red Excel.xlsx
-Movies
-Music
-NBA_players_2015.csv
-Overdue Customers 2.xlsx
-Oxamide_n2_water.agr
-Peer.ipynb
-Pictures
-Practice.ipynb
-Profile Picture.jpg
-Project.ipynb
-Prototype.ipynb
-Prototype_5.ipynb
-Public
-Quiz Review.ipynb
-README.md
-Reaction 1 Data.xlsx
-Reaction 2 Data.xlsx
-Reaction 3 Data.xlsx
-Reaction 4 Data.xlsx
-Red Cross - Wallet Card - Individual_SD-37055011.pdf
-Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf
-Review Lab_ Evan S..ipynb
-Review3_EvanS.ipynb
-Review_2.ipynb
-SAT__College_Board__2010_School_Level_Results.csv
-Sine and Cosine Curve.ipynb
-Split_2.tga
-SpotifyFinalProject.ipynb
-SulfurCys.agr
-TSLA.csv
-UNL.agr
-Untitled Folder
-Untitled.ipynb
-Untitled1.ipynb
-Untitled2.ipynb
-WAT_O.agr
-Working with OpenPyXL.xlsx
-anaconda3
-eclipse
-eclipse-workspace
-final_project_draft4.ipynb
-helloWorld.py
-install.sh
-introdata.ipynb
-java.log.34001
-java.log.37118
-job_skills.csv
-jupyter_mac.command
-matlab_crash_dump.6196-1
-miniconda3
-multiplot.agr
-opt
-plotting-with-pandas.ipynb
-population-by-country-2020.zip
-population_by_country_2020.csv
-rmsd.agr
-source.venv
-test.encrypted
-test.txt
-twitter-workshop-master.zip
-(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login1 ~]$ home
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd 4s0v/
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ cd no_charge/
-(base) [ehspector@login1 no_charge]$ ls
-s0v_no_hydrogens_no_charges.mol2  gas_2.in  gas_2.out  gas.out_scored.mol2
-(base) [ehspector@login1 no_charge]$ cd ..
-(base) [ehspector@login1 gas_teiger]$ vi no_gas.in
-(base) [ehspector@login1 gas_teiger]$ vi no_gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ cd ..
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd GA_data/
-(base) [ehspector@login1 GA_data]$ ls
-First_gen_data  Last_gen_data
-(base) [ehspector@login1 GA_data]$ cd ..
-(base) [ehspector@login1 4s0v]$ cd gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login1 ~]$ home
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd gas_test/
-(base) [ehspector@login1 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@login1 gas_test]$ cd ..
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd 4s0v/
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd s
--bash: cd: s: No such file or directory
-(base) [ehspector@login1 4s0v]$ cd structure/
-(base) [ehspector@login1 structure]$ ls
-s0v_ligand_hydrogens_charges.mol2        4s0v_no_hydrogens_no_charges.mol2
-s0v_ligand_no_hydrogens_no_charges.mol2  4s0v_protein_with_charges.mol2
-(base) [ehspector@login1 structure]$ cd ..
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd ..
-(base) [ehspector@login1 espector]$ cd gas_test/
-(base) [ehspector@login1 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@login1 gas_test]$ cd gas_f_test/
-(base) [ehspector@login1 gas_f_test]$ ls
-diff.out   gas_0.out_scored.mol2  gas_1.out              gas_50.in   gas_50.out_scored.mol2
-gas_0.out  gas_1.in               gas_1.out_scored.mol2  gas_50.out
-(base) [ehspector@login1 gas_f_test]$ vi gas_1.in
-(base) [ehspector@login1 gas_f_test]$ cd ..
-(base) [ehspector@login1 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@login1 gas_test]$ cd ..
-(base) [ehspector@login1 espector]$ cd 4s0v/gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ module
-Modules Release 4.0.0 (2017-10-16)
-Usage: module [options] [command] [args ...]
-Loading / Unloading commands:
-  add | load      modulefile [...]  Load modulefile(s)
-  rm | unload     modulefile [...]  Remove modulefile(s)
-  purge                             Unload all loaded modulefiles
-  reload | refresh                  Unload then load all loaded modulefiles
-  switch | swap   [mod1] mod2       Unload mod1 and load mod2
-Listing / Searching commands:
-  list            [-t|-l]           List loaded modules
-  avail   [-d|-L] [-t|-l] [mod ...] List all or matching available modules
-  aliases                           List all module aliases
-  whatis          [modulefile ...]  Print whatis information of modulefile(s)
-  apropos | keyword | search  str   Search all name and whatis containing str
-Collection of modules handling commands:
-  save            [collection|file] Save current module list to collection
-  restore         [collection|file] Restore module list from collection or file
-  saverm          [collection]      Remove saved collection
-  saveshow        [collection|file] Display information about collection
-  savelist        [-t|-l]           List all saved collections
-Shell's initialization files handling commands:
-  initlist                          List all modules loaded from init file
-  initadd         modulefile [...]  Add modulefile to shell init file
-  initrm          modulefile [...]  Remove modulefile from shell init file
-  initprepend     modulefile [...]  Add to beginning of list in init file
-  initswitch      mod1 mod2         Switch mod1 with mod2 from init file
-  initclear                         Clear all modulefiles from init file
-Other commands:
-  help            [modulefile ...]  Print this or modulefile(s) help info
-  display | show  modulefile [...]  Display information about modulefile(s)
-  test            [modulefile ...]  Test modulefile(s)
-  use     [-a|-p] dir [...]         Add dir(s) to MODULEPATH variable
-  unuse           dir [...]         Remove dir(s) from MODULEPATH variable
-  path            modulefile        Print modulefile path
-  paths           modulefile        Print path of matching available modules
-  source          scriptfile [...]  Execute scriptfile(s)
-Switches:
-  -t | --terse    Display output in terse format
-  -l | --long     Display output in long format
-  -d | --default  Only show default versions available
-  -L | --latest   Only show latest versions available
-  -a | --append   Append directory to MODULEPATH
-  -p | --prepend  Prepend directory to MODULEPATH
-Options:
-  -h | --help     This usage info
-  -V | --version  Module version
-  -D | --debug    Enable debug messages
-(base) [ehspector@login1 gas_teiger]$ module list
-Currently Loaded Modulefiles:
-) slurm/17.11.12   2) shared
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ cd ..
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd structure/
-(base) [ehspector@login1 structure]$ ls
-s0v_ligand_hydrogens_charges.mol2        4s0v_no_hydrogens_no_charges.mol2
-s0v_ligand_no_hydrogens_no_charges.mol2  4s0v_protein_with_charges.mol2
-(base) [ehspector@login1 structure]$ cd ..
-(base) [ehspector@login1 4s0v]$ cd gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ cd ..
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ vi gas_teiger/
-(base) [ehspector@login1 4s0v]$ cd gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ cd ..
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd energy_min/
-(base) [ehspector@login1 energy_min]$ ls
-s0v.lig.min_scored.mol2  min.in  min.out
-(base) [ehspector@login1 energy_min]$ cd ..
-(base) [ehspector@login1 4s0v]$ cd ..
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd 4s0v/
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ vi gas_teiger/
-(base) [ehspector@login1 4s0v]$ cd gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ vi gas.
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ cd ..
-(base) [ehspector@login1 4s0v]$ cd surface_spheres/
-(base) [ehspector@login1 surface_spheres]$ ls
-s0v_binding_spheres.sph  4s0v_surface.dms  INSPH  OUTSPH  selected_spheres.sph
-(base) [ehspector@login1 surface_spheres]$ cd ..
-(base) [ehspector@login1 4s0v]$ cd ..
-(base) [ehspector@login1 espector]$ cd gas_test/
-(base) [ehspector@login1 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@login1 gas_test]$ cd ..
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd 4s0v/
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd surface_spheres/
-(base) [ehspector@login1 surface_spheres]$ ls
-s0v_binding_spheres.sph  4s0v_surface.dms  INSPH  OUTSPH  selected_spheres.sph
-(base) [ehspector@login1 surface_spheres]$ cd ..
-(base) [ehspector@login1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login1 4s0v]$ cd gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ vi gas.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
-(base) [ehspector@login1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out
-(base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ class
-(base) [ehspector@login2 2025]$ ls
-additional_files
-(base) [ehspector@login2 2025]$ cd additional_files/
-(base) [ehspector@login2 additional_files]$ ls
-sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  touch.sh
-(base) [ehspector@login2 additional_files]$ vi sample_bashrc_4seawulf.txt
-(base) [ehspector@login2 additional_files]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login2 espector]$ cd builds/
-(base) [ehspector@login2 builds]$ cd alpha_branch/
-(base) [ehspector@login2 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@login2 alpha_branch]$ cd install/
-(base) [ehspector@login2 install]$ ls
-bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
-bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
-config.h   gnu.parallel        ibmaix                   Makefile        test
-configure  gnu.parallel.rdkit  intel                    oneapi
-docker     gnu.rdkit           intel.intelmpi.parallel  pgi
-gnu        gnu.valgrind        intel.ip.mkl             rules.h
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ l
-bash: l: command not found...
-(base) [ehspector@login2 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@login2 alpha_branch]$ cd install/
-(base) [ehspector@login2 install]$ ls
-bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
-bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
-config.h   gnu.parallel        ibmaix                   Makefile        test
-configure  gnu.parallel.rdkit  intel                    oneapi
-docker     gnu.rdkit           intel.intelmpi.parallel  pgi
-gnu        gnu.valgrind        intel.ip.mkl             rules.h
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@login2 alpha_branch]$ cd bin/
-(base) [ehspector@login2 bin]$ ls
-dock6  dock6.rdkit
-(base) [ehspector@login2 bin]$ vi dock6.rdkit
-(base) [ehspector@login2 bin]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd src/
-(base) [ehspector@login2 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@login2 src]$ vi Makefile
-(base) [ehspector@login2 src]$ cd rdkit/
-(base) [ehspector@login2 rdkit]$ ls
-boost         boost_1_71_0.tar.gz  eigen-3.3.9.tar.gz  rdkit-Release_2019_09_1
-boost_1_71_0  eigen-3.3.9          Makefile            rdkit-Release_2019_09_1.tar.gz
-(base) [ehspector@login2 rdkit]$ vi Makefile
-(base) [ehspector@login2 rdkit]$ vi Makefile
-(base) [ehspector@login2 rdkit]$ vi Makefile
-(base) [ehspector@login2 rdkit]$ ls
-boost         boost_1_71_0.tar.gz  eigen-3.3.9.tar.gz  rdkit-Release_2019_09_1
-boost_1_71_0  eigen-3.3.9          Makefile            rdkit-Release_2019_09_1.tar.gz
-(base) [ehspector@login2 rdkit]$ module list
-Currently Loaded Modulefiles:
-) slurm/17.11.12   2) shared
-(base) [ehspector@login2 rdkit]$ module load git
-WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
- /cm/local/apps/environment-modules/4.0.0//bin
-(base) [ehspector@login2 rdkit]$ module list
-Currently Loaded Modulefiles:
-) slurm/17.11.12   2) shared   3) git/2.36.2
-(base) [ehspector@login2 rdkit]$ git branch
-* alpha_branch
-  master
-(base) [ehspector@login2 rdkit]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25
-(base) supremestudier@Evans-MBP Spring_25 % ls
-AMS_500		AMS_537		AMS_691
-AMS_536		AMS_548		CARS_551
-(base) supremestudier@Evans-MBP Spring_25 % cd AMS_691
-(base) supremestudier@Evans-MBP AMS_691 % ls
-AMS691_01.pdf	Projects	Text_book
-(base) supremestudier@Evans-MBP AMS_691 % mkdir Lectures
-(base) supremestudier@Evans-MBP AMS_691 % cd ..
-(base) supremestudier@Evans-MBP Spring_25 % cd AMS_500
-(base) supremestudier@Evans-MBP AMS_500 % ls
-.06.08_hadjiargyrou.pdf
-(base) supremestudier@Evans-MBP AMS_500 % mkdir Materials
-(base) supremestudier@Evans-MBP AMS_500 % mv 2010.06.08_hadjiargyrou.pdf Materials
-(base) supremestudier@Evans-MBP AMS_500 % ls
-Materials
-(base) supremestudier@Evans-MBP AMS_500 % cd ..
-(base) supremestudier@Evans-MBP Spring_25 % cd CARS_551
-(base) supremestudier@Evans-MBP CARS_551 % ls
-(base) supremestudier@Evans-MBP CARS_551 % cd ..
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login2 espector]$ cd gas_test/
-(base) [ehspector@login2 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@login2 gas_test]$ cd ..
-(base) [ehspector@login2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login2 espector]$ cd 4s0v/
-(base) [ehspector@login2 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login2 4s0v]$ cd structure/
-(base) [ehspector@login2 structure]$ ls
-s0v_ligand_hydrogens_charges.mol2        4s0v_no_hydrogens_no_charges.mol2
-s0v_ligand_no_hydrogens_no_charges.mol2  4s0v_protein_with_charges.mol2
-(base) [ehspector@login2 structure]$ cd ..
-(base) [ehspector@login2 4s0v]$ cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
-(base) [ehspector@login2 4s0v]$ cd gas_teiger/
-(base) [ehspector@login2 gas_teiger]$ ls
-s0v_ligand_hydrogens_charges.mol2  gas.out              no_charge  no_gas.out
-gas.in                              gas.out_scored.mol2  no_gas.in  no_gas.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2
-(base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2
-(base) [ehspector@login2 gas_teiger]$ pwd
-/gpfs/projects/rizzo/espector/4s0v/gas_teiger
-(base) [ehspector@login2 gas_teiger]$ ls
-s0v_ligand_hydrogens_charges.mol2  gas.out              no_charge  no_gas.out
-gas.in                              gas.out_scored.mol2  no_gas.in  no_gas.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ cd no_charge/
-(base) [ehspector@login2 no_charge]$ ls
-s0v_no_hydrogens_no_charges.mol2  gas_2.in  gas_2.out  gas.out_scored.mol2
-(base) [ehspector@login2 no_charge]$ vi gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ cd ..
-(base) [ehspector@login2 gas_teiger]$ mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
-(base) [ehspector@login2 gas_teiger]$ cd no_charge/
-(base) [ehspector@login2 no_charge]$ ls
-s0v_ligand_hydrogens_charges.mol2  gas_2.in   gas.out_scored.mol2
-s0v_no_hydrogens_no_charges.mol2   gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@login2 no_charge]$ ls
-s0v_ligand_hydrogens_charges.mol2  gas_2.in   gas.out_scored.mol2
-s0v_no_hydrogens_no_charges.mol2   gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@login2 no_charge]$ ls
-s0v_ligand_hydrogens_charges.mol2  gas_2.in   gas.out_scored.mol2
-s0v_no_hydrogens_no_charges.mol2   gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.out
-(base) [ehspector@login2 no_charge]$ mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
-(base) [ehspector@login2 no_charge]$ ls
-s0v_ligand_hydrogens_no_charges.mol2  gas_2.in   gas.out_scored.mol2
-s0v_no_hydrogens_no_charges.mol2      gas_2.out
-(base) [ehspector@login2 no_charge]$ cd ..
-(base) [ehspector@login2 gas_teiger]$ cd ..
-(base) [ehspector@login2 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
-(base) [ehspector@login2 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/
-(base) [ehspector@login2 no_charge]$ ls
-s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
-s0v.lig.min_scored.mol2               gas_2.out
-s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
-(base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2
-(base) [ehspector@login2 no_charge]$ vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2
-files to edit
-(base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2
-(base) [ehspector@login2 no_charge]$ mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@login2 no_charge]$ ls
-s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
-s0v.lig_no_charge.min_scored.mol2     gas_2.out
-s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
-(base) [ehspector@login2 no_charge]$ vi gas_2.out
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ vi gas.out_scored.mol2
-(base) [ehspector@login2 no_charge]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ cd 4s0v/
-(base) [ehspector@login2 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/
-(base) [ehspector@login2 no_charge]$ vi gas_2.in
-(base) [ehspector@login2 no_charge]$ vi 4s0v.lig_no_charge.min_scored.mol2
-(base) [ehspector@login2 no_charge]$ vi gas_2.out
-(base) [ehspector@login2 no_charge]$ cd ..
-(base) [ehspector@login2 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login2 gas_teiger]$ vi gas.in
-(base) [ehspector@login2 gas_teiger]$ vi gas.out
-(base) [ehspector@login2 gas_teiger]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
+===Seawulf===
+	To complete this tutorial as a Stony Brook student, you will need an account on Seawulf. A ticket to obtain an account can be [https://rci.stonybrook.edu/HPC/faqs/requesting-a-seawulf-or-li-red-account submitted on the Seawulf website]; Dr. Rizzo will need to provide approval for account activation.
-Pushed a login request to your device...
+	The Seawulf website also has a [https://rci.stonybrook.edu/HPC/faqs/getting-started?field_hpc_cluster_target_id=All list of best practices] for using a High Performance Computing (HPC) cluster. We recommend reading through them before attempting to run any intensive programs on Seawulf. Of particular note is the job management system SLURM - we provide a full tutorial on this system in section 008 of this tutorial if you want to read up on it now, but it will not be necessary for this tutorial until that point.
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login2 espector]$ cd 4s0v/
-(base) [ehspector@login2 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@login2 4s0v]$ cd gas_teiger/
-(base) [ehspector@login2 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@login2 gas_teiger]$ vi no_gas.in
-(base) [ehspector@login2 gas_teiger]$ vi no_gas.out
-(base) [ehspector@login2 gas_teiger]$ vi no_gas.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+===SSH===
+You will need to use a Secure Shell (SSH) connection to connect to Seawulf remotely. A guide to this process is [https://rci.stonybrook.edu/HPC/faqs/logging-into-seawulf available on the Seawulf website].
-. Duo Push to XXX-XXX-9204
+===Basic Unix Commands and Environment===
+	Seawulf uses a terminal-based Unix operating system. If you have never used a terminal-based OS before, you should familiarize yourself with some [https://info-ee.surrey.ac.uk/Teaching/Unix/index.html basic Unix tutorials]. Broadly, you should know how to:
-Passcode or option (1-1): 1
+* List your working directory with <code>pwd</code>, change your working directory with <code>cd</code>, make new directories with <code>mkdir</code>, remove directories with <code>rmdir</code>, and list the contents of a directory with <code>ls</code>
+* Edit files using the text editor <code>vim</code> (use the <code>vimtutor</code> to read about basic functionality)
+* Create an empty file with <code>touch</code>, move files and directories around with <code>mv</code>, copy directories and files with <code>cp</code>, and (very carefully!) remove directories and files with <code>rm</code>
+* Determine if commands are available with <code>which</code>
+* Understand how to use commands and how flags/input parameters should be formatted
-Pushed a login request to your device...
+You should also understand the concept of filepaths, and how they are used by commands. Much of DOCK relies on you using the correct filepaths to pass files and parameters into the program, and if the paths are wrong, then the program will not work. When possible, it is advisable to use '''absolute''' filepaths (paths that start at the root directory), as opposed to paths relative to your current working directory. For example, if you are in the directory  <code>/gpfs/home/yourusername/tutorial/002_spheres</code>, referencing the absolute path <code>/gpfs/home/yourusername/tutorial/001_structure/important_structure.pdb</code> for a needed structure file is more reliable than the relative path <code>../001_structure/important_structure.pdb</code>, as the latter path is relative to <code>002_spheres/</code>, and meaningless outside of that context. The command <code>realpath</code>will return the absolute path of any file passed to it, which is useful for quickly and accurately determining the absolute path of any file.
-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:
+To work with DOCK6, it may also be necessary to add a path to your config file that tells Unix where to look for DOCK-related commands. You can check if you need to do this using the command <code>which dock6</code>. If <code>which</code> informs you that no <code>dock6</code> can be found, you will need to edit your .bashrc file:
+#Move to your home directory by either entering <code>cd</code> or <code>cd ~</code>
+#Use the command <code>vi .bashrc</code> to start editing your personal config file
+#At the bottom of the file, add the following line:
+<code>export PATH=$PATH:/Path/To/Your/DOCK6/bin</code>
-. Duo Push to XXX-XXX-9204
+where Path/To/Your/DOCK6/ should be replaced with whatever the path is to your local DOCK installation (note: the full path should end with /bin). At the time of this writing, there is a compiled version of DOCK6.12 at /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/, but if this does not work then ask Dr. Rizzo or a lab member where a compiled instance can be found
-Passcode or option (1-1): 1
+:4. Save and exit the file, then enter the command <code>source .bashrc</code> into the terminal.
+:5. Now when you request <code>which dock6</code>, the terminal should return the path to the directory you just provided.
-Pushed a login request to your device...
+After all this, you should have a good understanding of how to navigate the Unix terminal, and have the DOCK6 suite ready to use in your environment.
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ 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:
+=== SCP File Transfer ===
+	Another important aspect of working on Seawulf is uploading and downloading files to your local machine. This is accomplished using the Secure Copy Protocol (scp) terminal command. See the pertinent section on the [https://rci.stonybrook.edu/hpc/faqs/transferring-files-to-and-from-seawulf Seawulf website]. For Windows, it may be advisable to download a third party program; [https://filezilla-project.org/ FileZilla] works for this task.
-. Duo Push to XXX-XXX-9204
+===Directory setup===
+	Finally, assuming all necessary base Unix knowledge has been obtained, you will want to set up a set of directories for the work you will be doing in this tutorial. The directories will help you compartmentalize your work and help to prevent important files from being overwritten or lost. For the modules of this tutorial, we recommend setting up this directory structure, and setting up folders on your local machine with the same names for ease of file transfer:
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login1 ~]$ home
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd builds/
-(base) [ehspector@login1 builds]$ ls
-alpha_branch  dock6-master  dock6-master.zip  dock6-rdkit
-(base) [ehspector@login1 builds]$ cd alpha_branch/
-(base) [ehspector@login1 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@login1 alpha_branch]$ module load git
-WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
- /cm/local/apps/environment-modules/4.0.0//bin
-(base) [ehspector@login1 alpha_branch]$ git branch
-* alpha_branch
-  master
-(base) [ehspector@login1 alpha_branch]$ git config --get remote.origin.url
-https://github.com/EvanS-Dock6/dock6.git
-(base) [ehspector@login1 alpha_branch]$ git pull
-Username for 'https://github.com': EvanS_Dock6
-Password for 'https://EvanS_Dock6@github.com':
-remote: Support for password authentication was removed on August 13, 2021.
-remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
-fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
-(base) [ehspector@login1 alpha_branch]$ git pull
-Username for 'https://github.com': EvanS-Dock6
-Password for 'https://EvanS-Dock6@github.com':
-remote: Support for password authentication was removed on August 13, 2021.
-remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
-fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
-(base) [ehspector@login1 alpha_branch]$ git pull
-Username for 'https://github.com': EvanS-Dock6
-Password for 'https://EvanS-Dock6@github.com':
-remote: Enumerating objects: 1129, done.
-remote: Counting objects: 100% (672/672), done.
-remote: Compressing objects: 100% (147/147), done.
-remote: Total 1129 (delta 585), reused 561 (delta 525), pack-reused 457 (from 1)
-Receiving objects: 100% (1129/1129), 1.09 MiB | 13.11 MiB/s, done.
-Resolving deltas: 100% (909/909), completed with 45 local objects.
-From https://github.com/EvanS-Dock6/dock6
-be5c842..2ce698b4  alpha_branch -> origin/alpha_branch
-ce88e6..da80bfc9  master       -> origin/master
-Updating 4be5c842..2ce698b4
-error: Your local changes to the following files would be overwritten by merge:
-	src/dock/dock.cpp
-	src/dock/orient.cpp
-	src/dock/sphere.cpp
-Please commit your changes or stash them before you merge.
-Aborting
-(base) [ehspector@login1 alpha_branch]$ git status
-On branch alpha_branch
-Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
-  (use "git pull" to update your local branch)
-Changes not staged for commit:
-  (use "git add/rm <file>..." to update what will be committed)
-  (use "git restore <file>..." to discard changes in working directory)
-	deleted:    install/test/minimization/minimize7.dockout
-	modified:   src/dock/dock.cpp
-	modified:   src/dock/filter.cpp
-	modified:   src/dock/filter.h
-	modified:   src/dock/gasteiger.cpp
-	modified:   src/dock/orient.cpp
-	modified:   src/dock/sphere.cpp
-	modified:   src/rdkit/Makefile
-Untracked files:
-  (use "git add <file>..." to include in what will be committed)
-	src/dock/lol
-	src/rdkit/boost/
-	src/rdkit/boost_1_71_0.tar.gz
-	src/rdkit/boost_1_71_0/
-	src/rdkit/eigen-3.3.9.tar.gz
-	src/rdkit/eigen-3.3.9/
-	src/rdkit/rdkit-Release_2019_09_1.tar.gz
-	src/rdkit/rdkit-Release_2019_09_1/
-no changes added to commit (use "git add" and/or "git commit -a")
-(base) [ehspector@login1 alpha_branch]$ git diff src/dock/dock.cpp
-diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp
-index 81925eac..e447b601 100644
---- a/src/dock/dock.cpp
-+++ b/src/dock/dock.cpp
-@@ -820,7 +820,7 @@ main(int argc, char **argv)
-         if (c_filter.use_database_filter)
-         {
-             //calculate RDKIT-related descriptors for the ligand
--            c_filter.calc_descriptors(mol);
-+            c_filter.calc_descriptors(mol, c_typer);
-             //other descriptors are now computed & printed in amber_typer.cpp
-             //print out the descriptors
-             //cout << c_filter.get_descriptors(mol);
-(base) [ehspector@login1 alpha_branch]$ git diff src/dock/gasteiger.cpp
-diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
-index 5cfba835..3a967b89 100644
---- a/src/dock/gasteiger.cpp
-+++ b/src/dock/gasteiger.cpp
-@@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {
-     //Fochmod
-     //printf("gasteiger mark #1 \n");
--
-+        cout << "The for loop is initiated" << endl;
-     for (int a = 0; a < mol.num_atoms; a++) {
-         //printf("switchloop %d  \n", a);
-         switch (mol.atom_envs[a][1]) {
-@@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {
-                 param_b[a]     = 9.18;
-                 param_c[a]     = 1.88;
-                 param_d[a]     = param_a[a] + param_b[a] + param_c[a];
-+                cout << "This is the charge" << endl;
-                 break;
-             case 'B':   //C.2  trtrtr pi
-                 tot_charges[a] = 0.0;
-(base) [ehspector@login1 alpha_branch]$ git diff src/dock/orient.cpp
-diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
-index 92d58f71..2d63fece 100644
---- a/src/dock/orient.cpp
-+++ b/src/dock/orient.cpp
-@@ -461,8 +461,7 @@ Orient::get_spheres()
-     spheres = Active_Site_Spheres :: get_instance();
-     num_spheres = spheres.size();
--    if (verbose) cout << "Read in " << num_spheres
--                      << " spheres for orienting." << endl;
-+    cout << "Read in " << num_spheres << " spheres for orienting." << endl;
-     // process critical points
-     if (critical_points) {
-(base) [ehspector@login1 alpha_branch]$ git diff src/dock/sphere.cpp
-diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
-index 27641d83..5739a67c 100644
---- a/src/dock/sphere.cpp
-+++ b/src/dock/sphere.cpp
-@@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
-     fclose(sphere_file);
-     return num_spheres;
-+
- }
-(base) [ehspector@login1 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@login1 alpha_branch]$ cd src/dock
-(base) [ehspector@login1 dock]$ vi gasteiger.cpp
-(base) [ehspector@login1 dock]$ git diff gasteiger.cpp
-diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
-index 5cfba835..3a967b89 100644
---- a/src/dock/gasteiger.cpp
-+++ b/src/dock/gasteiger.cpp
-@@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {
-     //Fochmod
-     //printf("gasteiger mark #1 \n");
--
-+        cout << "The for loop is initiated" << endl;
-     for (int a = 0; a < mol.num_atoms; a++) {
-         //printf("switchloop %d  \n", a);
-         switch (mol.atom_envs[a][1]) {
-@@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {
-                 param_b[a]     = 9.18;
-                 param_c[a]     = 1.88;
-                 param_d[a]     = param_a[a] + param_b[a] + param_c[a];
-+                cout << "This is the charge" << endl;
-                 break;
-             case 'B':   //C.2  trtrtr pi
-                 tot_charges[a] = 0.0;
-(base) [ehspector@login1 dock]$ vi gasteiger.cpp
-(base) [ehspector@login1 dock]$ git diff gasteiger.cpp
-diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
-index 5cfba835..e82d5397 100644
---- a/src/dock/gasteiger.cpp
-+++ b/src/dock/gasteiger.cpp
-@@ -272,7 +272,6 @@ compute_gast_charges(DOCKMol & mol) {
-     //Fochmod
+First, create a tutorial directory in your home directory:
-     //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:
+<pre>
-  (use "git add <file>..." to update what will be committed)
+cd ~
-  (use "git restore <file>..." to discard changes in working directory)
+mkdir tutorial
-	modified:   gasteiger.cpp
+</pre>
-no changes added to commit (use "git add" and/or "git commit -a")
+Then, make a series of subdirectories inside of that tutorial directory:
-(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
+<pre>
-(base) [ehspector@login1 dock]$ git status
+cd ~/tutorial
-On branch alpha_branch
+mkdir 001_structure
-Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
+mkdir 002_spheres
-  (use "git pull" to update your local branch)
+mkdir 003_gridbox
+mkdir 004_energy_min
+mkdir 005_rigid_dock
+mkdir 006_flex_dock
+mkdir 007_footprint
+mkdir 008_virtual_screen
+mkdir 009_gen_alg
+mkdir 010_de_novo
+</pre>
-Changes not staged for commit:
+===A Note on Troubleshooting===
-  (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:
+	Finally, despite our best efforts at accuracy, a healthy amount of this tutorial will likely not go smoothly for you. There will be errors and inconsistencies between what you see here and what happens on Seawulf, and there may not be an immediate answer for what you should do to fix them. The instinct when this happens is to find someone who knows what might have happened and ask them for advice, and while this will usually be helpful, it may be inefficient. As such, we advise you to first please ''troubleshoot''. No program you will use in this tutorial is intended to be a black box. All of them do their best to return errors that tell you what is going wrong, and where to look to fix it. If you get an error, read it! Often it will tell you that it can't find a particular file ("doesn't exist" is the favorite wording), or that some piece of the input is giving it trouble— these tell you what paths to check or lines of a file to review. Also, copy-pasting an entire error into Google (or ChatGPT if you must) is a completely valid line of inquiry, and often yields helpful results.
-  (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")
+Having said that, here are some common errors and tactics you can use to fix them:
-(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:
+<code>"[File] could not be opened"</code> or <code>"[file] does not exist"</code> usually indicates that a path you gave the program is not accurate. You can "sanity check" paths by copying them directly from the input and putting them into an ls command. If it throws an error, fix the path!
-. Duo Push to XXX-XXX-9204
+<code>"version `GLIBCXX_whatever' not found"</code> is generally an issue with how the DOCK installation was compiled. Try to find a different version (/gpfs/projects/AMS536/zzz.programs usually has several versions available) or try running the command on a different node (Milan or Login)
-Passcode or option (1-1): 1
+Errors mentioning FORTRAAN: Make sure the input files are named correctly(ex INSPH for sphgen) and there are no extra spaces or lines anywhere in the input files. Sometimes they sneak in at the start or end of a line and are parsed literally.
-Pushed a login request to your device...
+Often, output is sent into a .out file instead of written to the console. If the program terminates immediately but does not return expected files, check whatever .out file was written for errors at the very bottom.
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ class
-(base) [ehspector@login2 2025]$ cd
-(base) [ehspector@login2 ~]$ ls
-class_project  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@login2 ~]$ mv class_project/ AMS_536
-(base) [ehspector@login2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@login2 ~]$ cd AMS_536/
-(base) [ehspector@login2 AMS_536]$ ls
-(base) [ehspector@login2 AMS_536]$ mkdir class_work
-(base) [ehspector@login2 AMS_536]$ mkdir class_project
-(base) [ehspector@login2 AMS_536]$ cd ..
-(base) [ehspector@login2 ~]$ cd AMS_536/
-(base) [ehspector@login2 AMS_536]$ pwd
-/gpfs/home/ehspector/AMS_536
-(base) [ehspector@login2 AMS_536]$ vi ~/.bashrc
-(base) [ehspector@login2 AMS_536]$ source ~/.bashrc
-(base) [ehspector@login2 AMS_536]$ home
-(base) [ehspector@login2 espector]$ class
-(base) [ehspector@login2 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@login2 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@login2 AMS_536]$ pwd
-/gpfs/home/ehspector/AMS_536
-(base) [ehspector@login2 AMS_536]$ cd ..
-(base) [ehspector@login2 ~]$ cd ..
-(base) [ehspector@login2 home]$ cd ..
-(base) [ehspector@login2 gpfs]$ cd projects/
-(base) [ehspector@login2 projects]$ ls
-ABCD                  EssigGroup            MaoGroup             SchedelGroup
-AllamGroup            FarhadzadehGroup      McDonoughGroup       SeeligerGroup
-AllenGroup            FernandezGroup        McGrewGroup          SehgalGroup
-AMS530                FernandezReuterGroup  McKinnonGroup        ShepsonGroup
-AMS536                FrenkelGroup          MehmoodGroup         SherGroup
-AMS598                FutcherGroup          MelikerGroup         SheridanGroup
-AMS691                GenomicsCore          MihalacheGroup       ShilkrotGroup
-Aponte-RiveraGroup    GergenGroup           MirandaGroup         SiegmannGroup
-ArmitageGroup         glimm                 MitchellGroup        SladeGroup
-AssanisGroup          GoblerGroup           MoellerGroup         SmaersGroup
-BEE690                GoldbartGroup         MofakhamGroup        SOC591
-BenchmarkGroup        HCPGroup              MohantyGroup         SOC595
-BenderGroup           HeinzGroup            MollProject          StanacevicGroup
-BernauerGroup         HollisterGroup        molssi               SternGroup
-BialkowskaGroup       HoltGroup             MoutsanidisGroup     SyritsynGroup
-BIO303                hpc_support           MujicaGroup          TakeuchiGroup
-BluesteinGroup        HudsonGroup           NadkarniGroup        TanGroup
-BurguenoGroup         IACSPDPGroup          NMRPIJodeyGroup      TaylorGroup
-CalderGroup           JiaoGroup             NMRPILipshultzGroup  TeraChemGroup
-CanliGroup            JohnsonGroup          NMRPIMingNgaiGroup   Tesse
-CarlsonGroup          JonesBozarthGroup     NMRPIPicartGroup     TestGroup1
-CascanteBonillaGroup  JonesGroup            OjimaGroup           ThackerGroup
-ChangGroup            JonesSkienaGroup      OkeomaGroup          ThakurGroup
-ChapmanGroup          KarzaiGroup           PadillaGroup         ThorneGroup
-CheCastaldoGroup      KeeGroup              PariseGroup          TitleGroup
-ChenGroup             KeeJiaoGroup          PercivalGroup        TsybychevGroup
-ChenXGroup            KellyGroup            PerlmanGroup         VanSnellenbergGroup
-CheungGroup           KhosronejadGroup      PernaGroup           VaskaGroup
-ChowdhuryGroup        KimGroup              PicartGroup          VeeramahGroup
-ChowdhuryRGroup       KirylukGroup          PiretGroup           VitekGroup
-ColleGroup            KodnerGroup           PolakGroup           VonDerLindenGroup
-CollierGroup          KogaGroup             PoonGroup            VorkasGroup
-CSE416                KozakovGroup          PowersGroup          WangGroup
-CSE504                KritzerGroup          PSY610               WanGroup
-CSE519                KrsticGroup           PSY620               WangXGroup
-CSE590                KrsticQuantumGroup    QuantComp            WeinachtGroup
-CSE628                KurcGroup             RahmeGroup           WeinsteinGroup
-DAndreaGroup          LeungGroup            RajputGroup          WeissmanGroup
-DavalosGroup          LevineGroup           RambowGroup          WilsonGroup
-DeLorenzoGroup        LiGroup               RestGroup            WymoreGroup
-DengYasarGroup        LoverdeGroup          ReuterGroup          YeGroup
-DevarajanGroup        LuGroup               RiosGroup            YouGroup
-DheillyGroup          LuhmannGroup          rizzo                ZhangGroup
-DillGroup             LuoGroup              rjh                  ZhanGroup
-DoboliGroup           LynchGroup            RosatiGroup          ZhangYGroup
-DubnauGroup           MaffeiGroup           samples              ZhaoGroup
-EBH370                MaGroup               SampsonCryoEMGroup   ZhouGroup
-EBH381                MakGroup              SampsonGroup         ZhouMedAdvGroup
-EkblomGroup           MallipattuGroup       SamulyakGroup        ZhuGroup
-(base) [ehspector@login2 projects]$ cd AMS536
-(base) [ehspector@login2 AMS536]$ cd zzz.programs
-(base) [ehspector@login2 zzz.programs]$ ls
-amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
-de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
-dock6.10         dock6.12         gen-frags-12         VS_libraries
-dock6.10_milan   dock6.12_ams536  old
-(base) [ehspector@login2 zzz.programs]$ cd dock6.12_ams536/
-(base) [ehspector@login2 dock6.12_ams536]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@login2 dock6.12_ams536]$ cd bin/
-(base) [ehspector@login2 bin]$ ls
-am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
-amberize_complex   espgen        nchemgrid_GB          showbox
-amberize_ligand    grid          nchemgrid_SA          showsphere
-amberize_receptor  grid-convert  parmcal               solvgrid
-antechamber        grid-convrds  parmchk               solvmap
-atomtype           make_phimap   prepare_amber.pl      sphere_selector
-bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
-chemgrid           mol2.py       prepgen               teLeap
-combine_torenv.py  mopac         resp                  tleap
-dock6              mopac.sh      respgen
-(base) [ehspector@login2 bin]$ cd
-(base) [ehspector@login2 ~]$ man date
-(base) [ehspector@login2 ~]$
-(base) [ehspector@login2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@login2 ~]$ cd ..
-(base) [ehspector@login2 home]$ cd ..
-(base) [ehspector@login2 gpfs]$ cd projects/AMS536/
-(base) [ehspector@login2 AMS536]$ ls
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@login2 AMS536]$ cd 2025/
-(base) [ehspector@login2 2025]$ ls
-additional_files  rotations
-(base) [ehspector@login2 2025]$ cd rotations/
-(base) [ehspector@login2 rotations]$ ls
-aokisamen
-(base) [ehspector@login2 rotations]$ cd ..
-(base) [ehspector@login2 2025]$ cd ..
-(base) [ehspector@login2 AMS536]$ ls
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@login2 AMS536]$ cd 2025/
-(base) [ehspector@login2 2025]$ ls
-additional_files  rotations
-(base) [ehspector@login2 2025]$ cd additional_files/
-(base) [ehspector@login2 additional_files]$ ls
-sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  test.txt  touch.sh
-(base) [ehspector@login2 additional_files]$ ls
-sample_bashrc_4seawulf.txt  sample_slurm_submission.sh  test.txt  touch.sh
-(base) [ehspector@login2 additional_files]$ cd ..
-(base) [ehspector@login2 2025]$ ls
-additional_files  rotations
-(base) [ehspector@login2 2025]$ cd ..
-(base) [ehspector@login2 AMS536]$ ls
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@login2 AMS536]$ vi junk.txt
-(base) [ehspector@login2 AMS536]$ ls
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@login2 AMS536]$ ls
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@login2 AMS536]$ cd 2025
-(base) [ehspector@login2 2025]$ ls
-additional_files  rotations  wed_fun.txt
-(base) [ehspector@login2 2025]$ ls
-additional_files  rotations  wed_humpday.txt
-(base) [ehspector@login2 2025]$ cd
-(base) [ehspector@login2 ~]$ cd ../../
-(base) [ehspector@login2 gpfs]$ sinfo
-PARTITION       AVAIL  TIMELIMIT  NODES  STATE NODELIST
-gpu                up    8:00:00      1  drain sn-nvda5
-gpu                up    8:00:00      5  alloc sn-nvda[3-4,6-8]
-p100               up 1-00:00:00      1  alloc cn-nvidia
-gpu-long           up 2-00:00:00      1  drain sn-nvda5
-gpu-long           up 2-00:00:00      5  alloc sn-nvda[3-4,6-8]
-gpu-large          up    8:00:00      1  drain sn-nvda5
-gpu-large          up    8:00:00      5  alloc sn-nvda[3-4,6-8]
-debug-28core       up    1:00:00      1  boot* sn046
-debug-28core       up    1:00:00      6 drain* sn[030-032,107-109]
-debug-28core       up    1:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
-debug-28core       up    1:00:00     12   idle sn[003-004,025-026,043-044,151-156]
-extended-28core    up 7-00:00:00      1  boot* sn046
-extended-28core    up 7-00:00:00      6 drain* sn[030-032,107-109]
-extended-28core    up 7-00:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
-extended-28core    up 7-00:00:00     12   idle sn[003-004,025-026,043-044,151-156]
-large-28core       up    8:00:00      1  boot* sn046
-large-28core       up    8:00:00      6 drain* sn[030-032,107-109]
-large-28core       up    8:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
-large-28core       up    8:00:00     12   idle sn[003-004,025-026,043-044,151-156]
-long-28core        up 2-00:00:00      1  boot* sn046
-long-28core        up 2-00:00:00      6 drain* sn[030-032,107-109]
-long-28core        up 2-00:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
-long-28core        up 2-00:00:00     12   idle sn[003-004,025-026,043-044,151-156]
-medium-28core      up   12:00:00      1  boot* sn046
-medium-28core      up   12:00:00      6 drain* sn[030-032,107-109]
-medium-28core      up   12:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
-medium-28core      up   12:00:00     12   idle sn[003-004,025-026,043-044,151-156]
-short-28core       up    4:00:00      1  boot* sn046
-short-28core       up    4:00:00      6 drain* sn[030-032,107-109]
-short-28core       up    4:00:00    137  alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
-short-28core       up    4:00:00     12   idle sn[003-004,025-026,043-044,151-156]
-v100               up 1-00:00:00      2   idle sn-nvda[1-2]
-(base) [ehspector@login2 gpfs]$ alias
-alias class='cd /gpfs/home/ehspector/AMS_536'
-alias egrep='egrep --color=auto'
-alias fgrep='fgrep --color=auto'
-alias grep='grep --color=auto'
-alias home='cd /gpfs/projects/rizzo/espector'
-alias l.='ls -d .* --color=auto'
-alias ll='ls -l --color=auto'
-alias ls='ls --color=auto'
-alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash'
-alias vi='vim'
-alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
-(base) [ehspector@login2 gpfs]$ class
-(base) [ehspector@login2 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@login2 AMS_536]$ cd class_work/
-(base) [ehspector@login2 class_work]$ ls
-(base) [ehspector@login2 class_work]$ touch Notes.txt
-(base) [ehspector@login2 class_work]$ vi Notes.txt
-(base) [ehspector@login2 class_work]$ vi Notes.txt
-(base) [ehspector@login2 class_work]$ vi Notes.txt
-(base) [ehspector@login2 class_work]$ class
-(base) [ehspector@login2 AMS_536]$ cd ..
-(base) [ehspector@login2 ~]$ class
-(base) [ehspector@login2 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@login2 AMS_536]$ cd class_work/
-(base) [ehspector@login2 class_work]$ ls
-Notes.txt
-(base) [ehspector@login2 class_work]$ vi Notes.txt
-(base) [ehspector@login2 class_work]$ vi Notes.txt
-(base) [ehspector@login2 class_work]$ alias
-alias class='cd /gpfs/home/ehspector/AMS_536'
-alias egrep='egrep --color=auto'
-alias fgrep='fgrep --color=auto'
-alias grep='grep --color=auto'
-alias home='cd /gpfs/projects/rizzo/espector'
-alias l.='ls -d .* --color=auto'
-alias ll='ls -l --color=auto'
-alias ls='ls --color=auto'
-alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash'
-alias vi='vim'
-alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
-(base) [ehspector@login2 class_work]$ which dock6
-/gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6
-(base) [ehspector@login2 class_work]$ vi Notes.txt
-(base) [ehspector@login2 class_work]$ vi ~/.bashrc
-(base) [ehspector@login2 class_work]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP PHYS_561 % cd
-(base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_500
-(base) supremestudier@Evans-MBP AMS_500 % ls
-Materials
-(base) supremestudier@Evans-MBP AMS_500 % mkdir Week_2
-(base) supremestudier@Evans-MBP AMS_500 % which python
-/Users/supremestudier/anaconda3/bin/python
-(base) supremestudier@Evans-MBP AMS_500 % pip install polaris-lib
-Collecting polaris-lib
-  Obtaining dependency information for polaris-lib from https://files.pythonhosted.org/packages/5f/69/3a9d76a53ebc41245755a71968e7789c543fe93cb48fff5b0a0a54aff56b/polaris_lib-0.11.6-py3-none-any.whl.metadata
-  Downloading polaris_lib-0.11.6-py3-none-any.whl.metadata (5.9 kB)
-Collecting authlib (from polaris-lib)
-  Obtaining dependency information for authlib from https://files.pythonhosted.org/packages/e8/6a/e83a6c04f8c6014c33d97c135782a55370cf60513f8d9f99f1279c7f9c13/Authlib-1.4.1-py2.py3-none-any.whl.metadata
-  Downloading Authlib-1.4.1-py2.py3-none-any.whl.metadata (3.9 kB)
-Collecting boto3<1.36.0 (from polaris-lib)
-  Obtaining dependency information for boto3<1.36.0 from https://files.pythonhosted.org/packages/65/77/8bbca82f70b062181cf0ae53fd43f1ac6556f3078884bfef9da2269c06a3/boto3-1.35.99-py3-none-any.whl.metadata
-  Downloading boto3-1.35.99-py3-none-any.whl.metadata (6.7 kB)
-Collecting datamol>=0.12.1 (from polaris-lib)
-  Obtaining dependency information for datamol>=0.12.1 from https://files.pythonhosted.org/packages/d4/e7/3df58df1af04dcc694a6c970e7138ba3ec3447a442deb427914438326107/datamol-0.12.5-py3-none-any.whl.metadata
-  Downloading datamol-0.12.5-py3-none-any.whl.metadata (8.0 kB)
-Collecting fastpdb (from polaris-lib)
-  Obtaining dependency information for fastpdb from https://files.pythonhosted.org/packages/ff/e3/be3b68743930f079776cdfa7d6475278c2160f77d2610fd4e98a1ae1c545/fastpdb-1.3.1-cp311-cp311-macosx_10_12_x86_64.whl.metadata
-  Downloading fastpdb-1.3.1-cp311-cp311-macosx_10_12_x86_64.whl.metadata (1.9 kB)
-Requirement already satisfied: fsspec[http] in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (2023.4.0)
-Collecting httpx (from polaris-lib)
-  Obtaining dependency information for httpx from https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl.metadata
-  Downloading httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
-Collecting numcodecs[msgpack]>=0.13.1 (from polaris-lib)
-  Obtaining dependency information for numcodecs[msgpack]>=0.13.1 from https://files.pythonhosted.org/packages/55/9c/5a540965c87f1d553748114734bf808d396e629080d4432e745adee02f09/numcodecs-0.15.0-cp311-cp311-macosx_10_9_x86_64.whl.metadata
-  Downloading numcodecs-0.15.0-cp311-cp311-macosx_10_9_x86_64.whl.metadata (2.9 kB)
-Requirement already satisfied: numpy<2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (1.24.3)
-Requirement already satisfied: pandas in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (2.0.3)
-Requirement already satisfied: pyarrow<18 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from polaris-lib) (11.0.0)
-Collecting pydantic>=2 (from polaris-lib)
-  Obtaining dependency information for pydantic>=2 from https://files.pythonhosted.org/packages/f4/3c/8cc1cc84deffa6e25d2d0c688ebb80635dfdbf1dbea3e30c541c8cf4d860/pydantic-2.10.6-py3-none-any.whl.metadata
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-Collecting pydantic-settings>=2 (from polaris-lib)
-  Obtaining dependency information for pydantic-settings>=2 from https://files.pythonhosted.org/packages/b4/46/93416fdae86d40879714f72956ac14df9c7b76f7d41a4d68aa9f71a0028b/pydantic_settings-2.7.1-py3-none-any.whl.metadata
-  Downloading pydantic_settings-2.7.1-py3-none-any.whl.metadata (3.5 kB)
-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)
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-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)
-  Obtaining dependency information for typing-extensions>=4.12.0 from https://files.pythonhosted.org/packages/26/9f/ad63fc0248c5379346306f8668cda6e2e2e9c95e01216d2b8ffd9ff037d0/typing_extensions-4.12.2-py3-none-any.whl.metadata
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-Collecting zarr<3,>=2 (from polaris-lib)
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-Collecting botocore<1.36.0,>=1.35.99 (from boto3<1.36.0->polaris-lib)
-  Obtaining dependency information for botocore<1.36.0,>=1.35.99 from https://files.pythonhosted.org/packages/fc/dd/d87e2a145fad9e08d0ec6edcf9d71f838ccc7acdd919acc4c0d4a93515f8/botocore-1.35.99-py3-none-any.whl.metadata
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-Collecting s3transfer<0.11.0,>=0.10.0 (from boto3<1.36.0->polaris-lib)
-  Obtaining dependency information for s3transfer<0.11.0,>=0.10.0 from https://files.pythonhosted.org/packages/66/05/7957af15543b8c9799209506df4660cba7afc4cf94bfb60513827e96bed6/s3transfer-0.10.4-py3-none-any.whl.metadata
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-  Obtaining dependency information for loguru from https://files.pythonhosted.org/packages/0c/29/0348de65b8cc732daa3e33e67806420b2ae89bdce2b04af740289c5c6c8c/loguru-0.7.3-py3-none-any.whl.metadata
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-  Obtaining dependency information for selfies from https://files.pythonhosted.org/packages/d8/28/e55116335f778c734b1211d3abacd429599a2f0f664d267eb1282f9906a2/selfies-2.2.0-py3-none-any.whl.metadata
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-  Obtaining dependency information for importlib-resources from https://files.pythonhosted.org/packages/a4/ed/1f1afb2e9e7f38a545d628f864d562a5ae64fe6f7a10e28ffb9b185b4e89/importlib_resources-6.5.2-py3-none-any.whl.metadata
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-  Obtaining dependency information for annotated-types>=0.6.0 from https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl.metadata
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-Building wheels for collected packages: asciitree
-  Building wheel for asciitree (setup.py) ... done
-  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5032 sha256=24fc75d0363ae85814cc0078da13ef4692220652876b36186c2bc8fd449fbede
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-Successfully built asciitree
-Installing collected packages: pyroaring, asciitree, typing-extensions, shellingham, selfies, numpy, loguru, importlib-resources, h11, fasteners, deprecated, annotated-types, scipy, rdkit, pydantic-core, numcodecs, httpcore, botocore, zarr, typer, s3transfer, pydantic, httpx, biotraj, authlib, pydantic-settings, datamol, boto3, biotite, fastpdb, polaris-lib
-  Attempting uninstall: typing-extensions
-    Found existing installation: typing_extensions 4.7.1
-    Uninstalling typing_extensions-4.7.1:
-      Successfully uninstalled typing_extensions-4.7.1
-  Attempting uninstall: numpy
-    Found existing installation: numpy 1.24.3
-    Uninstalling numpy-1.24.3:
-      Successfully uninstalled numpy-1.24.3
-  Attempting uninstall: scipy
-    Found existing installation: scipy 1.11.1
-    Uninstalling scipy-1.11.1:
-      Successfully uninstalled scipy-1.11.1
-  Attempting uninstall: botocore
-    Found existing installation: botocore 1.29.76
-    Uninstalling botocore-1.29.76:
-      Successfully uninstalled botocore-1.29.76
-  Attempting uninstall: pydantic
-    Found existing installation: pydantic 1.10.8
-    Uninstalling pydantic-1.10.8:
-      Successfully uninstalled pydantic-1.10.8
-ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
-tables 3.8.0 requires blosc2~=2.0.0, which is not installed.
-tables 3.8.0 requires cython>=0.29.21, which is not installed.
-gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed.
-numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.4 which is incompatible.
-anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible.
-aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible.
-Successfully installed annotated-types-0.7.0 asciitree-0.3.3 authlib-1.4.1 biotite-1.1.0 biotraj-1.2.2 boto3-1.35.99 botocore-1.35.99 datamol-0.12.5 deprecated-1.2.18 fasteners-0.19 fastpdb-1.3.1 h11-0.14.0 httpcore-1.0.7 httpx-0.28.1 importlib-resources-6.5.2 loguru-0.7.3 numcodecs-0.15.0 numpy-1.26.4 polaris-lib-0.11.6 pydantic-2.10.6 pydantic-core-2.27.2 pydantic-settings-2.7.1 pyroaring-1.0.0 rdkit-2024.9.4 s3transfer-0.10.4 scipy-1.15.1 selfies-2.2.0 shellingham-1.5.4 typer-0.15.1 typing-extensions-4.12.2 zarr-2.18.4
-(base) supremestudier@Evans-MBP AMS_500 % polaris login
-[2025-01-31 19:47:50] INFO     Your browser has been opened to visit: external_client.py:149
-                               https://clerk.polarishub.io/oauth/auth
-                               orize?response_type=code&client_id=agQ
-                               P2xVM6JqMHvGc&redirect_uri=https%3A%2F
-                               %2Fpolarishub.io%2Foauth2%2Fcallback&s
-                               cope=profile+email&state=YEjoNaFiIPI4k
-                               rv6quFJFVgB09TcYM&code_challenge=QG1cf
-                               HPgkiyqBUkzPRKUxet5FXo5xZWG21Lh_QXjhSU
-                               &code_challenge_method=S256
-Please enter the authorization token: 013927
-╭─────────────────────────── Traceback (most recent call last) ────────────────────────────╮
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/cli.py:31 in login  │
-│                                                                                          │
-│   28 │   This CLI will use the OAuth2 protocol to gain token-based access to the Polaris │
-│   29 │   """                                                                             │
-│   30 │   client = PolarisHubClient(settings=PolarisHubSettings(_env_file=client_env_file │
-│ ❱ 31 │   client.login(auto_open_browser=auto_open_browser, overwrite=overwrite)          │
-│   32                                                                                     │
-│   33                                                                                     │
-│   34 @app.command(hidden=True)                                                           │
-│                                                                                          │
-│ ╭──────────────────────────────────── locals ─────────────────────────────────────╮      │
-│ │ auto_open_browser = True                                                        │      │
-│ │            client = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │      │
-│ │   client_env_file = '.env'                                                      │      │
-│ │         overwrite = False                                                       │      │
-│ ╰─────────────────────────────────────────────────────────────────────────────────╯      │
-│                                                                                          │
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/client.py:249   │
-│ in login                                                                                 │
-│                                                                                          │
-│   246 │   │   │   auto_open_browser: Whether to automatically open the browser to visit  │
-│   247 │   │   """                                                                        │
-│   248 │   │   if overwrite or self.token is None or not self.ensure_active_token():      │
-│ ❱ 249 │   │   │   self.external_client.interactive_login(overwrite=overwrite, auto_open_ │
-│   250 │   │   │   self.token = self.fetch_token()                                        │
-│   251 │   │                                                                              │
-│   252 │   │   logger.info("You are successfully logged in to the Polaris Hub.")          │
-│                                                                                          │
-│ ╭──────────────────────────────────── locals ─────────────────────────────────────╮      │
-│ │ auto_open_browser = True                                                        │      │
-│ │         overwrite = False                                                       │      │
-│ │              self = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │      │
-│ ╰─────────────────────────────────────────────────────────────────────────────────╯      │
-│                                                                                          │
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │
-│ .py:158 in interactive_login                                                             │
-│                                                                                          │
-│   155 │   │   authorization_code = input("Please enter the authorization token: ")       │
-│   156 │   │                                                                              │
-│   157 │   │   # Step 3: Exchange authorization code for an access token                  │
-│ ❱ 158 │   │   self.fetch_token(code=authorization_code, grant_type="authorization_code") │
-│   159 │   │                                                                              │
-│   160 │   │   logger.info(f"Successfully authenticated to the Polaris Hub as `{self.user │
-│   161                                                                                    │
-│                                                                                          │
-│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
-│ │                  _ = 'YEjoNaFiIPI4krv6quFJFVgB09TcYM'                                │ │
-│ │ authorization_code = '013927'                                                        │ │
-│ │  authorization_url = 'https://clerk.polarishub.io/oauth/authorize?response_type=cod… │ │
-│ │  auto_open_browser = True                                                            │ │
-│ │          overwrite = False                                                           │ │
-│ │               self = <polaris.hub.external_client.ExternalAuthClient object at       │ │
-│ │                      0x1356cad90>                                                    │ │
-│ │     token_is_valid = False                                                           │ │
-│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
-│                                                                                          │
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │
-│ .py:74 in fetch_token                                                                    │
-│                                                                                          │
-│    71 │   def fetch_token(self, **kwargs) -> dict:                                       │
-│    72 │   │   """Light wrapper to automatically pass in the right URL"""                 │
-│    73 │   │   try:                                                                       │
-│ ❱  74 │   │   │   return super().fetch_token(                                            │
-│    75 │   │   │   │   url=self.settings.token_fetch_url, code_verifier=self.code_verifie │
-│    76 │   │   │   )                                                                      │
-│    77 │   │   except OAuth2Error as error:                                               │
-│                                                                                          │
-│ ╭──────────────────────────────────── locals ─────────────────────────────────────╮      │
-│ │ kwargs = {'code': '013927', 'grant_type': 'authorization_code'}                 │      │
-│ │   self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │      │
-│ ╰─────────────────────────────────────────────────────────────────────────────────╯      │
-│                                                                                          │
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:21 │
-│ 7 in fetch_token                                                                         │
-│                                                                                          │
-│   214 │   │   if url is None:                                                            │
-│   215 │   │   │   url = self.metadata.get('token_endpoint')                              │
-│   216 │   │                                                                              │
-│ ❱ 217 │   │   return self._fetch_token(                                                  │
-│   218 │   │   │   url, body=body, auth=auth, method=method,                              │
-│   219 │   │   │   headers=headers, **session_kwargs                                      │
-│   220 │   │   )                                                                          │
-│                                                                                          │
-│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
-│ │                   auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2Cli… │ │
-│ │                          object at 0x136f50190>                                      │ │
-│ │ authorization_response = None                                                        │ │
-│ │                   body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2F… │ │
-│ │             grant_type = 'authorization_code'                                        │ │
-│ │                headers = {                                                           │ │
-│ │                          │   'Accept': 'application/json',                           │ │
-│ │                          │   'Content-Type':                                         │ │
-│ │                          'application/x-www-form-urlencoded;charset=UTF-8'           │ │
-│ │                          }                                                           │ │
-│ │                 kwargs = {                                                           │ │
-│ │                          │   'code_verifier':                                        │ │
-│ │                          'S2qmBfN72W2onFO2So06MzNLUB8yVXmHmp4m9xisHaIUA9zU',         │ │
-│ │                          │   'code': '013927'                                        │ │
-│ │                          }                                                           │ │
-│ │                 method = 'POST'                                                      │ │
-│ │                   self = <polaris.hub.external_client.ExternalAuthClient object at   │ │
-│ │                          0x1356cad90>                                                │ │
-│ │         session_kwargs = {}                                                          │ │
-│ │                  state = None                                                        │ │
-│ │                    url = 'https://clerk.polarishub.io/oauth/token'                   │ │
-│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
-│                                                                                          │
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:37 │
-│ 9 in _fetch_token                                                                        │
-│                                                                                          │
-│   376 │   │   for hook in self.compliance_hook['access_token_response']:                 │
-│   377 │   │   │   resp = hook(resp)                                                      │
-│   378 │   │                                                                              │
-│ ❱ 379 │   │   return self.parse_response_token(resp)                                     │
-│   380 │                                                                                  │
-│   381 │   def _refresh_token(self, url, refresh_token=None, body='', headers=None,       │
-│   382 │   │   │   │   │      auth=None, **kwargs):                                       │
-│                                                                                          │
-│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
-│ │    auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2ClientAuth object   │ │
-│ │           at 0x136f50190>                                                            │ │
-│ │    body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2Fpolarishub.io%2… │ │
-│ │ headers = {                                                                          │ │
-│ │           │   'Accept': 'application/json',                                          │ │
-│ │           │   'Content-Type': 'application/x-www-form-urlencoded;charset=UTF-8'      │ │
-│ │           }                                                                          │ │
-│ │  kwargs = {}                                                                         │ │
-│ │  method = 'POST'                                                                     │ │
-│ │    resp = <Response [401 Unauthorized]>                                              │ │
-│ │    self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90>     │ │
-│ │     url = 'https://clerk.polarishub.io/oauth/token'                                  │ │
-│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
-│                                                                                          │
-│ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:35 │
-│ 5 in parse_response_token                                                                │
-│                                                                                          │
-│   352 │   │                                                                              │
-│   353 │   │   token = resp.json()                                                        │
-│   354 │   │   if 'error' in token:                                                       │
-│ ❱ 355 │   │   │   raise self.oauth_error_class(                                          │
-│   356 │   │   │   │   error=token['error'],                                              │
-│   357 │   │   │   │   description=token.get('error_description')                         │
-│   358 │   │   │   )                                                                      │
-│                                                                                          │
-│ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
-│ │  resp = <Response [401 Unauthorized]>                                                │ │
-│ │  self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90>       │ │
-│ │ token = {                                                                            │ │
-│ │         │   'error': 'invalid_grant',                                                │ │
-│ │         │   'error_description': 'The provided authorization grant (e.g.,            │ │
-│ │         authorization code, resource owner crede'+156                                │ │
-│ │         }                                                                            │ │
-│ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
-╰──────────────────────────────────────────────────────────────────────────────────────────╯
-OAuthError: invalid_grant: The provided authorization grant (e.g., authorization code,
-resource owner credentials) or refresh token is invalid, expired, revoked, does not match
-the redirection URI used in the authorization request, or was issued to another client
-(base) supremestudier@Evans-MBP AMS_500 % polaris login
-[2025-01-31 19:49:32] INFO     Your browser has been opened to visit: external_client.py:149
-                               https://clerk.polarishub.io/oauth/auth
-                               orize?response_type=code&client_id=agQ
-                               P2xVM6JqMHvGc&redirect_uri=https%3A%2F
-                               %2Fpolarishub.io%2Foauth2%2Fcallback&s
-                               cope=profile+email&state=qo1ea4ucZsaZS
-                               OGFfAWK47Skq0G4jU&code_challenge=irfzd
-                               YmRLZliQeiwg2GQYa156QMYqb4zXHNXQJFb0pE
-                               &code_challenge_method=S256
-Please enter the authorization token: MTLLNZK2ZWETMDBMMY0ZMGU5LWJJYZKTZWI5MZYWMDHIOTCZ
-[2025-01-31 19:49:45] INFO     Successfully authenticated to the      external_client.py:160
-                               Polaris Hub as
-                               `evan.spector@stonybrook.edu`! 🎉
-[2025-01-31 19:49:46] INFO     You are successfully logged in to the Polaris   client.py:252
-                               Hub.
-(base) supremestudier@Evans-MBP AMS_500 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-(base) [ehspector@login1 ~]$ home
-(base) [ehspector@login1 espector]$ module list
-Currently Loaded Modulefiles:
-) slurm/17.11.12   2) shared   3) gcc/13.2.0   4) mvapich2/gcc13.2/2.3.7   5) gcc-stack
-(base) [ehspector@login1 espector]$ module load git
-WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
- /cm/local/apps/environment-modules/4.0.0//bin
-(base) [ehspector@login1 espector]$ git diff
-warning: Not a git repository. Use --no-index to compare two paths outside a working tree
-usage: git diff --no-index [<options>] <path> <path>
-Diff output format options
+== 001: Structure Prep ==
-    -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
+=== Downloading the PDB ===
-    -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
+Having setup your necessary environment to work on Seawulf, let's navigate to your local computer and begin
-    --minimal             produce the smallest possible diff
+the protein preparation process:
-    -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
+To begin protein preparation you will need the 1O86 PDB file. Using this link: https://www.rcsb.org/structure/1O86,
-    --relative[=<prefix>]
+you will see the RCSB main page opened to our protein of choice:
-                          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
+[[File:1O86_RCSB_1.png|600px]]
-fatal: not a git repository (or any parent up to mount point /)
-Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-(base) [ehspector@login1 espector]$ git branch
-fatal: not a git repository (or any parent up to mount point /)
-Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ module list
-Currently Loaded Modulefiles:
-) slurm/17.11.12   3) gcc/13.2.0               5) gcc-stack
-) shared           4) mvapich2/gcc13.2/2.3.7   6) git/2.36.2
-(base) [ehspector@login1 espector]$ history
-  make rdkit
-  modue list
-  module list
-  module unload gcc
-  module list
-  module unload mvapich2/gcc13.2/2.3.7
-  module unload gcc-stack
-  module list
-  module load gcc/7.2.0
-  which gcc
-  make rdkitclean
-  make rdkit
-  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
-  vi ~/.bashrc
-  module list
-  ls
-  source ~/.bashrc
-  module list
-  ls
-  vi ~/.bashrc
-  make clean
-  ./configure gnu.rdkit
-  make dock
-  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
-  home
-  cd RDKit/gas/
-  ls
-  sbatch 4s0v_filter.slurm
-  vi 4s0v_filter.slurm
-  sbatch 4s0v_filter.slurm
-  squeue -u ehspector
-  vi 4s0v_filter.slurm
-  squeue -u ehspector
-  cd ..
-  cd 4s0v/
-  cd GA
-  ls
-  cd 4s0v_GA_results/
-  ls
-  vi 4s0v_GA_output.restart0000.mol2
-  vi 4s0v_GA_output.restart0001.mol2
-  cd ..
-  ls
-  cd virtual_screening/
-  ls
-  vi virtual.in
-  squeue -u ehspector
-  cd ..
-  cd RDKit/gas/
-  ls
-  vi filter_out.txt
-  cd ..
-  cd 4s0v/gas_teiger/
-  ls
-  touch gas_rdkit
-  dock6 -i gas_rdkit
-  which dock
-  vi ~/.bashrc
-  source ~/.bashrc
-  which dock
-  which rdkit
-  source ~/.bashrc
-  which dock6
-  which dock6.rdkit
-  vi ~/.bashrc
-  source ~/.bashrc
-  which dock6.rdkit
-  ls
-  dock6.rdkit -i gas_rdkit
-  rm gas_rdkit
-  cd ..
-  cd RDKit/
-  cd gas
-  sbatch 4s0v_filter.slurm
-  squeue -u ehspector
-  ls
-  squeue -u ehspector
-  ls
-  vi output_scored.mol2
-  squeue -u ehspector
-  vi output_scored.mol2
-  cd ..
-  vi output_scored.mol2
-  cd ..
-  cd 4s0v/
-  ls
-  cd GA_data/
-  ls
-  cd ..
-  cd GA
-  ls
-  cd ..
-  cd gas_teiger/
-  ls
-  touch gas_rd.in
-  dock6.rdkit gas_rd.in
-  cd ..
-  cd gas_teiger/
-  dock6 -i gas_rd.in
-  rm gas_rd.in
-  cd ..
-  ls
-  cd ..
-  cd builds/alpha_branch/src/dock
-  vi filter.cpp
-  cd ..
-  cd install/
-  make clean
-  make dock
-  ls
-  ./configure
-  ./configure gnu
-  make -i distclean
-  make dock
-  ./configure
-  ./configure gnu
-  make clean
-  ./configure gnu
-  make dock
-  module unload gcc/7.2.0
-  module load gcc-stack
-  make dock
-  cd ..
-  cd ../..
-  ls
-  cd 4s0v/gas_teiger/
-  ls
-  dock6 -i  gas.in
-  ls
-  vi gas.out_scored.mol2
-  cd ..
-  cd builds/alpha_branch/src/dock
-  ls
-  vi filter.cpp
-  cd ../..
-  cd install/
-  make clean
-  make dock
-  cd ../../..
-  cd 4s0v/gas_teiger/
-  dock6 -i gas.in
-  ls
-  vi gas.out_scored.mol2
-  cd ../..
-  cd builds/alpha_branch/src/dock
-  vi filter.cpp
-  cd ..]
-  cd ..
-  cd install/
-  make clean
-  make dock
-  make clean
-  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
-  home
-  module list
-  cd 4s0v/
-  ls
-  cd GA
-  ls
-  squeue -u ehspector
-  ls
-  cd 4s0v_GA_results/
-  ls
-  cd ..
-  ls
-  cd gas_test/
-  ls
-  vi test.in
-  dock6 -i test.in
-  ls
-  vi test.in
-  dock6 -i test.in
-  cd ..
-  cp 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/
-  ls
-  cd gas_test/
-  ls
-  mkdir gas_f_test
-  ls
-  cd ..
-  cp 4s0v/GA/4s0v_GA_results/4s0v_GA.slurm gas_test/gas_f_test/
-  cd gas_test/
-  mv gas_f_test/4s0v_GA.slurm gas_test
-  ls
-  cd gas_f_test/
-  ls
-  cd ..
-  mv gas_test 4s0v_GA.slurm
-  ls
-  vi 4s0v_GA.slurm
-  vi 4s0v_GA.in
-  cd ..
-  cd 4s0v/GA
-  ls
-  cd 4s0v_fraglib/
-  pwd
-  cd ..
-  cd gas_test/
-  ls
-  vi 4s0v_GA.in
-  cd ..
-  ls
-  cd ..
-  ls
-  cd zzz.programs/
-  ls
-  cd ..
-  cd espector/
-  ls
-  cd gas_test/
-  ls
-  vi 4s0v_GA.in
-  vi 4s0v_GA.slurm
-  vi 4s0v_GA.
-  vi 4s0v_GA.in
-  vi 4s0v_GA.slurm
-  sbatch 4s0v_GA.slurm
-  squeue -u ehspector
-  exit
-  squeue -u ehspector
-  exit
-  home
-  squeue -u ehspector
-  exir
-  exit
-  home
-  squeue -u ehspector
-  ls
-  cd gas_test/
-  ls
-  cd gas_f_test/
-  ls
-  cd ..
-  vi GA.txt
-  cd ..
-  ls
-  cd gas_test/
-  ls
-  vi 4s0v_GA.in
-  cd ..
-  cd 4s0v/GA
-  ls
-  cd 4s0v_
-  cd 4s0v_fraglib/
-  ls
-  cd ..
-  ls
-  cd 4s0v_GA_results/
-  ls
-  vi 4s0v_GA.in
-  cd ..
-  cd 4s0v_fraglib/
-  ls
-  cd ..
-  ls
-  cd ..
-  cd gas_test/
-  ls
-  vi 4s0v_GA.in
-  sbatch 4s0v_GA.slurm
-  squeue -u ehspector
-  home
-  cd gas_test/
-  ls
-  vi GA.txt
-  vi 4s0v_GA.in
-  cd ..
-  vimdiff 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/4s0v_GA.in
-  cd gas_test/
-  vi 4s0v_GA.in
-  sbatch 4s0v_GA.slurm
-  squeue -u ehspector
-  ls
-  vi GA.txt
-  vi 4s0v_GA.in
-  vi GA.txt
-  module list
-  cd ..
-  cd builds/
-  cd alpha_branch/src/dock
-  make clean
-  make dock
-  home
-  ls
-  cd RDKit/
-  ls
-  vi filter.in
-  cd
-  home
-  ls
-  cd RDKit/
-  ls
-  vi output_scored.mol2
-  cd gas/
-  ls
-  vi filter.in
-  cd gas_test/
-  ls
-  vi filter.in
-  vi output_scored.mol2
-  cd ..
-  home
-  ls
-  cd builds/alpha_branch/src/h
-  cd builds/alpha_branch/src/dock
-  cd ..
-  cd install
-  history
-  cd ..
-  cd install/
-  ./configure gnu
-  make clean
-  make dock
-  cd ..
-  ls
-  cd ..
-  ls
-  cd gas_test/
-  ls
-  vi 4s0v_GA.in
-  vi 4s0v_GA.slurm
-  sbatch 4s0v_GA.slurm
-  squeue -u ehspector
-  ls
-  vi GA.txt \
-  vi GA.txt
-  exit
-  home
-  ls
-  cd RDKit/
-  ls
-  cd gas/
-  ls
-  cd ..
-  cd gas_test/
-  ls
-  sbatch 4s0v_GA.slurm
-  vi 4s0v_GA.slurm
-  sbatch 4s0v_GA.slurm
-  squeue -u ehspector
-  ls
-  vi GA.txt
-  home
-  cd builds/alpha_branch/install/
-  make clean
-  ./configure gnu
-  cd ./install
-  make dock
-  cd ..
-  module list
-  module load gcc-stack
-  module list
-  cd ..
-  ls
-  cd gas_test/
-  ls
-  sbatch 4s0v_GA.slurm
-  squeue -u ehspector
-  ls
-  vi 4s0v_GA_output.restart0000.mol2
-  ls
-  module list
-  ls
-  squeue -u ehspector
-  ls
-  squeue -u ehspector
-  exit
-  home
-  ls
-  cd gas_test/
-  ls
-  cd ..
-  cp 4s0v/gas_teiger/gas.in gas_test/gas_f_test/
-  cd gas_test/gas_f_test/
-  ls
-  vi gas.in
-  cd ..
-  pwd
-  cd gas_f_test/
-  vi gas.in
-  dock6 -i gas.in -o gas_0.out
-  ls
-  vi gas.out_scored.mol2
-  vi gas_0.out
-  vi gas.in
-  dock6 -i gas.in -o gas_0.out
-  ls
-  vi gas.out_scored.mol2
-  cd ..
-  vimdiff 4s0v_GA_output.restart0000.mol2 gas_f_test/gas.out_scored.mol2
-  cd ..
-  cd gas_test/
-  vi 4s0v_GA_output.restart0000.mol2
-  cd gas_f_test/
-  ls
-  mv gas.out_scored.mol2 gas_0.out_scored.mol2
-  ls
-  vi gas.in
-  mv gas.in gas_1.in
-  dock6 -i gas_1.in -o gas_1.out
-  ls
-  mv gas.out_scored.mol2 gas_1.out_scored.mol2
-  vi gas_1.out_scored.mol2
-  cd ..
-  vi 4s0v_GA_output.restart0001.mol2
-  vi 4s0v_GA_output.restart0050.mol2
-  cd gas_f_test/
-  ls
-  cp gas_1.in gas_50.out
-  mv gas_50.out gas_50.in
-  vi gas_50.in
-  dock6 -i gas_50.in -o gas_50.out
-  ls
-  mv gas.out_scored.mol2 gas_50.out_scored.mol2
-  vi gas_50.out_scored.mol2
-  cd ..
-  vi 4s0v_GA_output.restart0050.mol2
-  cd gas_f_test/
-  vi gas_50.out_scored.mol2
-  cd ..
-  mkdir gas_RD_tes
-  mv gas_RD_tes/ gas_RD_Test/
-  ls
-  exit
-  make clean
-  make dock
-  cd ..
-  ls
-  home
-  ls
-  cd RDKit/
-  ls
-  vi filter
-  vi filter.in
-  cd gas
-  ls
-  vi filter.
-  vi filter.in
-  cd ..
-  cd RDKit/
-  cd gas/
-  ls
-  cd gas_test/
-  ls
-  cd ..
-  cp RDKit/gas/filter.in gas_test/gas_RD_Test/
-  cd RDKit/
-  ls
-  vi 4s0v_filter.slurm
-  cd ..
-  home
-  cd gas_test/
-  ls
-  cd gas_RD_Test/
-  ls
-  cd ..
-  cd gas_RD_Test/
-  ls
-  cd ..
-  cd gas_f_test/
-  ls
-  vi gas_0.in
-  vi gas_1.in
-  cd ..
-  cd gas_RD_Test/
-  vi filter.in
-  mv filter.in gas.in
-  dock6.rdkit -i gas.in -o gas.out
-  ls
-  vi output_scored.mol2
-  ls
-  vi gas.out
-  vi gas.in
-  dock6.rdkit -i gas.in -o gas.out
-  ls
-  vi gas.out
-  vi gas.in
-  exit
-  home
-  cd builds/alpha_branch/install/
-  make clean
-  ls
-  ./configure gnu.rdkit
-  make dock
-  module list
-  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
-  exit
-  dock6.rdkit -i gas_50.in -o gas_50.out
-  ls
-  grep -wc MOLECULE *.mol2
-  diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2
-  diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
-  vi diff.out
-  vi output_scored.mol2
-  cd ..
-  cd gas_f_test/
-  ls
-  grep -wc MOLECULE gas_50.out_scored.mol2
-  diff gas_50.out_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
-  vi diff.out
-  home
-  vi ~/.bashrc
-  source ~/.bashrc
-  exit
-  home
-  cd gas_test/
-  ls
-  cd gas_RD_Test/
-  ls
-  vi gas.out
-  vi output_scored.mol2
-  vi gas.in
-  vi output_scored.mol2
-  ls
-  cd ..
-  ls
-  grep -wc MOLECULE 4s0v_GA_output.restart0001.mol2
-  cd ..
-  ls
-  cd gas_test/
-  ls
-  cd gas_RD_Test/
-  ls
-  vi gas.out
-  vi output_rejected.mol2
-  cd ..
-  vimdiff 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2
-  diff 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2
-  diff -y 4s0v_GA_output.restart0001.mol2  gas_RD_Test/output_scored.mol2
-  cd gas_RD_Test/
-  ls
-  cp gas.in gas_50.in
-  vi gas_50.in
-  dock6.rdkit -i gas_50.in -o gas_50.out
-  dock6.rdkit -i gas.in -o gas.out
-  module list
-  srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
-  rd
-  vi ~/.bashrc
-  source ~/.bashrc
-  rd
-  home
-  ls
-  cd gas_test/
-  ls
-  cd gas_f_test/
-  vi diff.out
-  cd ..
-  cd gas_RD_test
-  ls
-  cd gas_RD_Test/
-  ls
-  vi diff.out
-  history
-  ls
-  vi output_scored.mol2
-  cd ..
-  cd gas_f_test/
-  ls
-  vi gas_50.out_scored.mol2
-  home
-  ls
-  cd builds/
-  ls
-  cd ..
-  ls
-  cd gas_test/gas_f_test/
-  ls
-  vi gas_50.out_scored.mol2
-  awk '{print $9}' gas_50.out_scored.mol2
-  :q
-  vi gas_50.out_scored.mol2
-  awk '{print $9}' gas_50.out_scored.mol2
-  :q
-  awk '{print $9}' gas_50.out_scored.mol2 > charges.txt
-  vi charges.txt
-  cd ..
-  cd gas_RD_Test/
-  ls
-  awk '{print $9}' output_scored.mol2 > RD_charges.txt
-  vi RD_charges.txt
-  ls
-  cd ..
-  ls
-  awk '{print $9}' 4s0v_GA_output.restart0050.mol2 > charges.txt
-  vi charges.txt
-  mkdir charge_data.txt
-  ls
-  mv charge_data.txt/ charge_data/
-  ls
-  mv charges.txt charge_data/
-  cd charge_data/
-  ls
-  mv charges.txt original_charges.txt
-  cd ..
-  ls
-  cd gas_f_test/
-  ls
-  mv charges.txt f_charges.txt
-  cd ..
-  mv gas_f_test/f_charges.txt charge_data/
-  ls
-  ls charge_data/
-  ls
-  cd gas_RD_Test/
-  ls
-  cd ..
-  mv gas_RD_Test/RD_charges.txt charge_data/
-  ls
-  exit
-  home
-  cd gas_test/
-  cd charge_data/
-  paste -d "," original_charges.txt f_charges.txt RD_charges.txt > gasteiger_charges.csv
-  vi gasteiger_charges.csv
-  vi original_charges.txt
-  cd ..
-  vi 4s0v_GA_output.restart0050.mol2
-  ls
-  cd charge_data/
-  ls
-  pwd
-  exit
-  home
-  cd ..
-  ls
-  cd AMS536
-  ls
-  cd 2025
-  ls
-  cd additional_files/
-  ls
-  cd ..
-  cd 2025
-  pwd
-  vi ~/.bashrc
-  home
-  source ~/.bashrc
-  class
-  home
-  ls
-  exit
-  home
-  ls
-  cd 4s0v/
-  ls
-  cd gas_teiger/
-  ls
-  cd no_charge/
-  ls
-  cd ..
-  vi no_gas.in
-  vi no_gas.out_scored.mol2
-  cd ..
-  ls
-  cd GA_data/
-  ls
-  cd ..
-  cd gas_teiger/
-  ls
-  vi gas.out_scored.mol2
-  exit
-  home
-  ls
-  cd gas_test/
-  ls
-  cd ..
-  ls
-  cd 4s0v/
-  ls
-  cd s
-  cd structure/
-  ls
-  cd ..
-  ls
-  cd ..
-  cd gas_test/
-  ls
-  cd gas_f_test/
-  ls
-  vi gas_1.in
-  cd ..
-  ls
-  cd ..
-  cd 4s0v/gas_teiger/
-  ls
-  vi gas.in
-  module
-  module list
-  ls
-  cd ..
-  ls
-  cd structure/
-  ls
-  cd ..
-  cd gas_teiger/
-  ls
-  vi gas.in
-  dock6 -i gas.in -o gas.out
-  ls
-  vi gas.out
-  vi gas.out_scored.mol2
-  cd ..
-  ls
-  vi gas_teiger/
-  cd gas_teiger/
-  ls
-  vi gas.in
-  dock6 -i gas.in -o gas.out
-  ls
-  vi gas.out
-  vi gas.out_scored.mol2
-  cd ..
-  ls
-  cd energy_min/
-  ls
-  cd ..
-  ls
-  cd 4s0v/
-  ls
-  vi gas_teiger/
-  cd gas_teiger/
-  vi gas.
-  vi gas.in
-  dock6 -i gas.in -o gas.out
-  ls
-  vi gas.out
-  vi gas.in
-  cd ..
-  cd surface_spheres/
-  ls
-  cd ..
-  cd gas_test/
-  ls
-  cd ..
-  ls
-  cd 4s0v/
-  ls
-  cd surface_spheres/
-  ls
-  cd ..
-  ls
-  cd gas_teiger/
-  ls
-  vi gas.in
-  dock6 -i gas.in -o gas.out
-  ls
-  vi gas.out
-  vi gas.out_scored.mol2
-  vi gas.in
-  dock6 -i gas.in -o gas.out
-  ls
-  vi gas.out
-  vi gas.out_scored.mol2
-  exit
-  home
-  class
-  ls
-  cd additional_files/
-  ls
-  vi sample_bashrc_4seawulf.txt
-  exit
-  home
-  ls
-  cd builds/
-  cd alpha_branch/
-  ls
-  cd install/
-  ls
-  cd ..
-  l
-  ls
-  cd install/
-  ls
-  cd ..
-  ls
-  cd bin/
-  ls
-  vi dock6.rdkit
-  cd ..
-  cd src/
-  ls
-  vi Makefile
-  cd rdkit/
-  ls
-  vi Makefile
-  ls
-  module list
-  module load git
-  module list
-  git branch
-  exit
-  home
-  ls
-  cd gas_test/
-  ls
-  cd ..
-  ls
-  cd 4s0v/
-  ls
-  cd structure/
-  ls
-  cd ..
-  cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
-  cd gas_teiger/
-  ls
-  vi 4s0v_ligand_hydrogens_charges.mol2
-  pwd
-  ls
-  cd no_charge/
-  ls
-  vi gas_2.out
-  vi gas_2.in
-  cd ..
-  mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
-  cd no_charge/
-  ls
-  vi gas_2.in
-  dock6 -i gas_2.in -o gas_2.out
-  vi gas_2.out
-  vi gas_2.in
-  dock6 -i gas_2.in -o gas_2.out
-  ls
-  vi gas_2.out
-  vi gas_2.in
-  dock6 -i gas_2.in -o gas_2.out
-  ls
-  vi gas_2.out
-  mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
-  ls
-  cd ..
-  cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
-  ls
-  cd gas_teiger/no_charge/
-  ls
-  vi 4s0v.lig.min_scored.mol2
-  vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2
-  vi 4s0v.lig.min_scored.mol2
-  mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
-  vi gas_2.in
-  dock6 -i gas_2.in -o gas_2.out
-  ls
-  vi gas_2.out
-  vi gas_2.in
-  vi gas.out_scored.mol2
-  exit
-  home
-  cd 4s0v/
-  ls
-  cd gas_teiger/no_charge/
-  vi gas_2.in
-  vi 4s0v.lig_no_charge.min_scored.mol2
-  vi gas_2.out
-  cd ..
-  ls
-  vi gas.in
-  vi gas.out
-  exit
-  home
-  ls
-  cd 4s0v/
-  ls
-  cd gas_teiger/
-  ls
-  vi no_gas.in
-  vi no_gas.out
-  vi no_gas.out_scored.mol2
-  exit
-  class
-  pwd
-  cd ..
-  vi ~/.bashrc
-  source ~/.bashrc
-  home
-  class
-  exit
-  class
-  mkdir ehspector
-  ls
-  cd ehspector/
-  ls
-  touch file.txt
-  ls
-  cd ..
-  cd
-  ls
-  mkdir class_project
-  ls
-  exit
-  home
-  ls
-  cd builds/
-  ls
-  cd alpha_branch/
-  ls
-  module load git
-  git branch
-  git config --get remote.origin.url
-  git pull
-  git status
-  git diff src/dock/dock.cpp
-  git diff src/dock/gasteiger.cpp
-  git diff src/dock/orient.cpp
-  git diff src/dock/sphere.cpp
-  ls
-  cd src/dock
-  vi gasteiger.cpp
-  git diff gasteiger.cpp
-  vi gasteiger.cpp
-  git diff gasteiger.cpp
-  git status gasteiger.cpp
-  vi gasteiger.cpp
-  git diff gasteiger.cpp
-  git status gasteiger.cpp
-  git status
-  git diff sphere.cpp
-  exit
-  home
-  class
-  cd
-  ls
-  mv class_project/ AMS_536
-  ls
-  cd AMS_536/
-  ls
-  mkdir class_work
-  mkdir class_project
-  cd ..
-  cd AMS_536/
-  pwd
-  vi ~/.bashrc
-  source ~/.bashrc
-  home
-  class
-  ls
-  pwd
-  cd ..
-  cd projects/
-  ls
-  cd AMS536
-  cd zzz.programs
-  ls
-  cd dock6.12_ams536/
-  ls
-  cd bin/
-  ls
-  cd
-  man date
-  ls
-  cd ..
-  cd projects/AMS536/
-  ls
-  cd 2025/
-  ls
-  cd rotations/
-  ls
-  cd ..
-  ls
-  cd 2025/
-  ls
-  cd additional_files/
-  ls
-  cd ..
-  ls
-  cd ..
-  ls
-  vi junk.txt
-  ls
-  cd 2025
-  ls
-  cd
-  cd ../../
-  sinfo
-  alias
-  class
-  ls
-  cd class_work/
-  ls
-  touch Notes.txt
-  vi Notes.txt
-  class
-  cd ..
-  class
-  ls
-  cd class_work/
-  ls
-  vi Notes.txt
-  which dock6
-  vi Notes.txt
-  vi ~/.bashrc
-  exit
-  home
-  module list
-  module load git
-  git diff
-  git status
-  git branch
-  ls
-  module list
-  history
-(base) [ehspector@login1 espector]$ git branch
-fatal: not a git repository (or any parent up to mount point /)
-Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-(base) [ehspector@login1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login1 espector]$ cd builds/alpha_branch/
-(base) [ehspector@login1 alpha_branch]$ git branch
-* alpha_branch
-  master
-(base) [ehspector@login1 alpha_branch]$ git status
-On branch alpha_branch
-Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
-  (use "git pull" to update your local branch)
-Changes not staged for commit:
+Next, you'll want to navigate to the top right corner where it says Download Files. Then, select the dropdown arrow.
-  (use "git add/rm <file>..." to update what will be committed)
+The following dropdown menu will appear on the screen:
-  (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")
+[[File:1O86_RCSB_2.png|600px]]
-(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:
+Select 'Legacy PDB Format'. Now the PDB file should be downloaded to your local computer.
-  (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")
+Now that you have the PDB file, lets navigate to Chimera program to open the file.
-(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:
+=== Protein Isolation ===
-  (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:
+Now that you have the downloaded PDB, the first step is to isolate and modify our protein, if necessary.
-  (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")
+First, open the PDB in Chimera using File >> Open, zoom into where the ligand is, hold the control key and click to select an atom on the ligand, and press the up arrow key to highlight the ligand. Then go to Actions >> Focus.
-(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:
+The ligand should now be highlighted in green; you will see it is surrounded by water molecules:
-  (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:
+[[File:Ligand_Embed.png|600px]]
-  (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")
+We're going to get rid of the ligand and the water molecules.
-(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
+First, since the ligand is highlighted, go to Actions >> Atoms/Bonds >> Delete.
-==> WARNING: A newer version of conda exists. <==
+There may be a glycine molecule remaining in the binding pocket. For the sake of simplicity, we are going to delete this as well. Control+click to select an atom in the glycine, up arrow to highlight the whole molecule, and Actions >> Atoms/Bonds >> Delete it in the same manner as the ligand.
-  current version: 23.7.4
-  latest version: 25.1.1
-Please update conda by running
+Next, to get rid of the water molecules, navigate to Select >> Residue >> HOH
-    $ conda update -n base -c defaults conda
+You'll notice that all of the water molecules are highlighted:
-Or to minimize the number of packages updated during conda update use
+[[File:Water.png|600px]]
-     conda install conda=25.1.1
+Just like the ligand, navigate to Actions >> Atoms/Bonds >> Delete
+Now you have just a protein:
-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
+[[File:Protein_only.png|600px]]
-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
+=== Inspecting the Protein ===
-(base) supremestudier@Evans-MBP AMS_500 % cd ..
+With just the protein file, lets inspect if there are any missing loops along the exterior. First, to make the view clearer, go to View >> Focus again to put the whole protein in focus.
-(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
+You'll notice that there is a missing loop between residues 434 and 439.
-All rights reserved.
-Redistribution and use in source and binary forms, with or without
+[[File:Missing_loop.png|600px]]
-modification, are permitted provided that the following conditions are met:
-* Redistributions of source code must retain the above copyright notice, this
+To refine the missing loop, go to Tools >> Structure Editing >> select Model/Refine Loops
-  list of conditions and the following disclaimer.
-* Redistributions in binary form must reproduce the above copyright notice,
+The following pop up menus will appear:
-  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
+[[File:Residue List.png|600px]]
-  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"
+This is a list of the residues in the protein. The residues 435-438 boxed in red denote the ones involved with the missing loop.
-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
+[[File:Model_refine.png|600px]]
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
+This is the Modeller/Refine Menu. If you have not used it before, the Modeller License Key field may be empty, which will prevent the program from running.
-ehspector@login.seawulf.stonybrook.edu's password:
+You will first need to register for a Modeller key [https://www.salilab.org/modeller/registration.html on the official page]. They will email you with the registration key relatively promptly (within a day but usually sooner). Note that because this program connects to a webserver for the loop modeling, you will require a stable internet connection to use it.
-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:
+You can leave all the other options selected as is. Once you select apply, wait a couple of minutes.
+The program is generating different refinements to the missing loops. The residue menu will say "Running Modeller Web Service".
+Additionally, you'll be able to track the process completed on the search bar menu on the bottom part of the screen on Chimera.
-. Duo Push to XXX-XXX-9204
+Once the modeler is 100% completed, the following popup menu will appear on Chimera:
-Passcode or option (1-1): 1
+[[File:Modeller_menu.png|600px]]
-Pushed a login request to your device...
+You can see that the modeller program generated five alternative protein models that refined the missing loop.
-Success. Logging you in...
+If you press the shift key and highlight all of the model numbers you will see the following proteins with fixed loops.
-(base) [ehspector@login1 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@login1 ~]$ cd AMS_536/
-(base) [ehspector@login1 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@login1 AMS_536]$ cd class_work/
-(base) [ehspector@login1 class_work]$ ls
-Notes.txt
-(base) [ehspector@login1 class_work]$ vi Notes.txt
-(base) [ehspector@login1 class_work]$ touch commands.txt
-(base) [ehspector@login1 class_work]$ vi commands.txt
-(base) [ehspector@login1 class_work]$ bash commands.txt
-(base) [ehspector@login1 class_work]$ ls
-_structure  commands.txt  Notes.txt
-(base) [ehspector@login1 class_work]$ vi commands.txt
-(base) [ehspector@login1 class_work]$ bash commands.txt
-mkdir: cannot create directory ‘001_structure’: File exists
-(base) [ehspector@login1 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@login1 class_work]$ exit
-logout
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+[[File:Fixed_loop.png|600px]]
-. Duo Push to XXX-XXX-9204
+Now, using the drop down menu, from earlier, you'll want to assess what's the best model to choose that has refined loops.
+Sometimes the difference in scores are negligible and you may want to select based on zDope, which would mean any loop is sufficient.
+However, there may be another score that could narrow your decision making.
-Passcode or option (1-1): 1
+In the 'Modeller Results' menu, select Fetch Scores. You'll see in your chimera window that a job was submitted.
+This is signaling to the program to retrieve the scores from the program. Once the job is finished, the Estimated RMSD
+and Estimated Overlap columns will contain values:
-Pushed a login request to your device...
+[[File:Scores.png|600px]]
-Success. Logging you in...
-(base) [ehspector@login1 ~]$ class
-(base) [ehspector@login1 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@login1 AMS_536]$ cd class_work/
-(base) [ehspector@login1 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@login1 class_work]$ cd 001_structure/
-(base) [ehspector@login1 001_structure]$ pwd
-/gpfs/home/ehspector/AMS_536/class_work/001_structure
-(base) [ehspector@login1 001_structure]$ ^C
-(base) [ehspector@login1 001_structure]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+From adding more scores, you'll notice that the models differ in their Estimated RMSD values. Based on these values,
+Models 1.2 or 1.5 are a good choice based on RMSD. So, let's choose model 1.2 as our protein model to use in this tutorial.
+We will also save this model as our new PDB file.
-. Duo Push to XXX-XXX-9204
+Go to File >> Save PDB. When the save menu appears, make sure that only the second model is selected like so:
-Passcode or option (1-1): 1
+[[File:Save_Menu.png|600px]]
-Pushed a login request to your device...
+Let's also give this PDB a new title, the one supplied is <code> 1O86_fixed_protein.pdb </code>. Additionally, we will need the original PDB for ligand preparation.
-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:
+Press save and now you have a refined protein to prepare.
-. Duo Push to XXX-XXX-9204
+=== Protein Preparation ===
-Passcode or option (1-1): 1
+After saving a protein with modelled loops as a PDB, use File >> Close Session to clear your Chimera session. Then, File >> Open the <code> 1O86_fixed_protein.pdb </code>
-Pushed a login request to your device...
+In order to use this protein for docking calculations, we will need to generate a charged, protonated protein and ligand files. Charged molecules must be saved in Mol2 format, as the PDB file format does not support partial atomic charges.
-Success. Logging you in...
-(base) [ehspector@login1 ~]$ class
-(base) [ehspector@login1 AMS_536]$ cd class_work/
-(base) [ehspector@login1 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@login1 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@login1 002_surface_spheres]$ ls
-w26_surface.dms
-(base) [ehspector@login1 002_surface_spheres]$ vi INSPH
-(base) [ehspector@login1 002_surface_spheres]$ vi INSPH
-(base) [ehspector@login1 002_surface_spheres]$ sphgen -i INSPH -o OUTSPH
-bash: sphgen: command not found...
-(base) [ehspector@login1 002_surface_spheres]$ which sphgen
-/usr/bin/which: no sphgen in (/gpfs/home/ehspector/miniconda3/bin:/gpfs/home/ehspector/miniconda3/condabin:/gpfs/software/mvapich/haswell/gcc13.2/2.3.7/bin:/gpfs/software/gcc/haswell/13.2.0/bin:/cm/shared/apps/slurm/17.11.12/sbin:/cm/shared/apps/slurm/17.11.12/bin:/cm/local/apps/environment-modules/4.0.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/4.0.0/bin:/gpfs/software/local/bin:/gpfs/projects/rizzo/espector/builds/alpha_branch/bin:/gpfs/home/ehspector/bin)
-(base) [ehspector@login1 002_surface_spheres]$ cd ..
-(base) [ehspector@login1 class_work]$ cd ..
-(base) [ehspector@login1 AMS_536]$ cd ..
-(base) [ehspector@login1 ~]$ cd ..
-(base) [ehspector@login1 home]$ cd ..
-(base) [ehspector@login1 gpfs]$ cd projects/AMS536
-(base) [ehspector@login1 AMS536]$ ls
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@login1 AMS536]$ cd 2025/
-(base) [ehspector@login1 2025]$ ls
-additional_files  robbashrc_file  rotations  wed_humpday.txt
-(base) [ehspector@login1 2025]$ cd ..
-(base) [ehspector@login1 AMS536]$ cd zzz.programs/
-(base) [ehspector@login1 zzz.programs]$ ls
-amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
-de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
-dock6.10         dock6.12         gen-frags-12         VS_libraries
-dock6.10_milan   dock6.12_ams536  old
-(base) [ehspector@login1 zzz.programs]$ cd dock6.12_ams536
-(base) [ehspector@login1 dock6.12_ams536]$ ls
-bin  developer  docs  install  parameters  README  README.md  src  template_pipeline  tutorials
-(base) [ehspector@login1 dock6.12_ams536]$ cd bin/
-(base) [ehspector@login1 bin]$ ls
-am1bcc             combine_torenv.py  mol2bild.py          parmchk               showsphere
-amberize_complex   dock6              mol2.py              prepare_amber.pl      solvgrid
-amberize_ligand    dock6.mpi          mopac                prepare_rna_amber.pl  solvmap
-amberize_receptor  espgen             mopac.sh             prepgen               sphere_selector
-antechamber        grid               multigrid_fp_gen.py  resp                  sphgen
-atomtype           grid-convert       nchemgrid_GB         respgen               teLeap
-bondtype           grid-convrds       nchemgrid_SA         sevsolv               tleap
-chemgrid           make_phimap        parmcal              showbox
-(base) [ehspector@login1 bin]$ pwd
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
-(base) [ehspector@login1 bin]$ class
-(base) [ehspector@login1 AMS_536]$ cd class_work/
-(base) [ehspector@login1 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@login1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen)
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
-(base) [ehspector@login1 002_surface_spheres]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+We will first save a version of the protein in Mol2 format that does not have any charges or hydrogens.
+Go to File >> Save Mol2. You will want to give this mol2 file a title that describes the fact that
+the protein doesn't have hydrogens or charges. So let's name this file <code> 1O86_protein_nH_ncH.mol2 </code>
-. Duo Push to XXX-XXX-9204
+The nH refers to "no hydrogens" and the ncH refers to "no charges".
-Passcode or option (1-1): 1
+Now that the mol2 is saved, we can protonate and charge the receptor in preparation for docking.
-Pushed a login request to your device...
+'''Adding Hydrogens'''
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd class_work/
-(base) [ehspector@milan1 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-w26_surface.dms  INSPH
-(base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
-At line 328 of file sphgen.f
-Fortran runtime error: Bad value during floating point read
-Error termination. Backtrace:
+Go to Tools >> Structure Editing >> AddH
-#0  0x7ffff7d59e39 in formatted_transfer_scalar_read
-	at ../../../libgfortran/io/transfer.c:1790
-#1  0x7ffff7d5b535 in formatted_transfer
-	at ../../../libgfortran/io/transfer.c:2491
-#2  0x4049e0 in ???
-#3  0x40516a in ???
-#4  0x40117c in ???
-#5  0x7ffff742958f in ???
-#6  0x7ffff742963f in ???
-#7  0x4011b4 in ???
-#8  0xffffffffffffffff in ???
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-w26_surface.dms  INSPH  OUTSPH  temp1.ms  temp3.atc
-(base) [ehspector@milan1 002_surface_spheres]$ rm 2w26_surface.dms
-(base) [ehspector@milan1 002_surface_spheres]$ rm temp1.ms temp3.atc
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-INSPH  OUTSPH
-(base) [ehspector@milan1 002_surface_spheres]$ rm OUTSPH
-(base) [ehspector@milan1 002_surface_spheres]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+The following menu will appear:
-. Duo Push to XXX-XXX-9204
+[[File:wm.png|600px]]
-Passcode or option (1-1): 1
+All the defaults that are selected are acceptable. Select OK.
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd class_work
-(base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-w26_new_surface.dms  INSPH
-(base) [ehspector@milan1 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH
-(base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH
-(base) [ehspector@milan1 002_surface_spheres]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Permission denied, please try again.
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+You will get a confirmation message on the chimera text bar that says 'Hydrogens Added'.
+Now you have added hydrogens to the protein file. The last thing to do is to add charges.
-. Duo Push to XXX-XXX-9204
+'''Adding Charges'''
-Passcode or option (1-1): 1
+Before we can save the second mol2 for the protein we must also add charges to the protein.
-Pushed a login request to your device...
+Go to Tools >> Structure Editing >> press Add Charge
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ module load git
-(base) [ehspector@milan2 ~]$ home
-(base) [ehspector@milan2 espector]$ cd builds/
-(base) [ehspector@milan2 builds]$ cd alpha_branch/
-(base) [ehspector@milan2 alpha_branch]$ git branch
-* alpha_branch
-  master
-(base) [ehspector@milan2 alpha_branch]$ git pull
-/gpfs/software/git/2.36.2/libexec/git-core/git-remote-https: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory
-(base) [ehspector@milan2 alpha_branch]$ module list
-Currently Loaded Modulefiles:
-) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack
-) shared                   4) mvapich2/gcc13.2/2.3.7   6) git/2.36.2
-(base) [ehspector@milan2 alpha_branch]$ module unload git
-(base) [ehspector@milan2 alpha_branch]$ git pull
-Username for 'https://github.com': EvanS-Dock6
-Password for 'https://EvanS-Dock6@github.com':
-Updating 4be5c842..2ce698b4
-error: Your local changes to the following files would be overwritten by merge:
-	src/dock/dock.cpp
-	src/dock/orient.cpp
-Please commit your changes or stash them before you merge.
-Aborting
-(base) [ehspector@milan2 alpha_branch]$ git status
-On branch alpha_branch
-Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
-  (use "git pull" to update your local branch)
-Changes not staged for commit:
+The following menu will appear:
-  (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:
+[[File:cm.png|600px]]
-  (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")
+By default Chimera selects AM1-BCC charges, but for this tutorial we are going to use Gasteiger charges.
-(base) [ehspector@milan2 alpha_branch]$ git add
+Every other selection on the menu is okay, so after changing the charge type, go ahead and select apply. You'll notice another pop up menu appears:
-Nothing specified, nothing added.
-hint: Maybe you wanted to say 'git add .'?
-hint: Turn this message off by running
-hint: "git config advice.addEmptyPathspec false"
-(base) [ehspector@milan2 alpha_branch]$ git add src/dock/dock.cpp src/dock/filter.cpp src/dock/filter.h
-(base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: ability to gasterize mols"
-[alpha_branch 8c38cd54] feat: ability to gasterize mols
-files changed, 70 insertions(+), 8 deletions(-)
-(base) [ehspector@milan2 alpha_branch]$ git status
-On branch alpha_branch
-Your branch and 'origin/alpha_branch' have diverged,
-and have 1 and 267 different commits each, respectively.
-  (use "git pull" if you want to integrate the remote branch with yours)
-Changes not staged for commit:
+[[File:specify.png|600px]]
-  (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:
+This deals with ions. Just as before, make sure that Gasteiger is selected. All other defaults are okay.
-  (use "git add <file>..." to include in what will be committed)
+Select OK. The Chimera window will inform you that standard charges are added.
-	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")
+Now that your protein has hydrogens and charges, we can go ahead and generate the second mol2 file.
-(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:
+Go to File >> Save Mol2. This time the name should reflect that the protein has hydrogens and charges.
-  (use "git add/rm <file>..." to update what will be committed)
+Let's name it <code> 1O86_protein_wH_wcH.mol2 </code>.
-  (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:
+Now our protein files are prepared for docking, let's now turn our attention to preparing the ligand.
-  (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")
+=== Isolating the Ligand ===
-(base) [ehspector@milan2 alpha_branch]$ git add  src/dock/orient.cpp
-(base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: shows number of spheres generated"
-[alpha_branch 704ff10f] feat: shows number of spheres generated
-file changed, 3 insertions(+), 3 deletions(-)
-(base) [ehspector@milan2 alpha_branch]$ git add src/rdkit/Makefile
-(base) [ehspector@milan2 alpha_branch]$ git commit -m "fix: replaces boost url with working one "
-[alpha_branch 123e4913] fix: replaces boost url with working one
-file changed, 3 insertions(+), 1 deletion(-)
-(base) [ehspector@milan2 alpha_branch]$ git status
-On branch alpha_branch
-Your branch and 'origin/alpha_branch' have diverged,
-and have 3 and 267 different commits each, respectively.
-  (use "git pull" if you want to integrate the remote branch with yours)
-Changes not staged for commit:
+Having made a Protein PDB and generated two mol2 files, lets now do the same thing for the ligand. The first step is to File >> Close Session to clear the current environment, then open the original PDB file that we downloaded.
-  (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:
+Just like in the protein section, press control and select an atom on the ligand. Then press the up arrow to highlight the entire ligand:
-  (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")
+[[File:Ligand_Embed.png|600px]]
-(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:
+Go to Select >> Invert (selected models)
-  (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:
+[[File:all_highlight.png|600px]]
-  (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")
+You'll notice that everything around the ligand is highlighted.
-(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:
+Now go to Actions >> Atoms/Bonds >> delete
-  (use "git restore --staged <file>..." to unstage)
-	deleted:    install/test/minimization/minimize7.dockout
-Untracked files:
+Now we have a file that just contains the ligand.
-  (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"
+[[File:1O86_ligand.png|600px]]
-[alpha_branch fe018e1e] build: rm minimize.docot
-file changed, 187 deletions(-)
- delete mode 100644 install/test/minimization/minimize7.dockout
-(base) [ehspector@milan2 alpha_branch]$ git push
-Username for 'https://github.com': ^C
-(base) [ehspector@milan2 alpha_branch]$ git pull
-Username for 'https://github.com': EvanS-Dock6
-Password for 'https://EvanS-Dock6@github.com':
-hint: You have divergent branches and need to specify how to reconcile them.
-hint: You can do so by running one of the following commands sometime before
-hint: your next pull:
-hint:
-hint:   git config pull.rebase false  # merge
-hint:   git config pull.rebase true   # rebase
-hint:   git config pull.ff only       # fast-forward only
-hint:
-hint: You can replace "git config" with "git config --global" to set a default
-hint: preference for all repositories. You can also pass --rebase, --no-rebase,
-hint: or --ff-only on the command line to override the configured default per
-hint: invocation.
-fatal: Need to specify how to reconcile divergent branches.
-(base) [ehspector@milan2 alpha_branch]$ git pull --rebase
-Username for 'https://github.com': EvanS-Dock6
-Password for 'https://EvanS-Dock6@github.com':
-Successfully rebased and updated refs/heads/alpha_branch.
-(base) [ehspector@milan2 alpha_branch]$ git status
-On branch alpha_branch
-Your branch is ahead of 'origin/alpha_branch' by 4 commits.
-  (use "git push" to publish your local commits)
-Untracked files:
+Go to File >> Save PDB and name the file <code> 1O86_ligand.pdb </code>
-  (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)
+This will be the file that we will use to prepare the mol2 files for the dock program.
-(base) [ehspector@milan2 alpha_branch]$ git push
-Username for 'https://github.com': EvanS-Dock6
-Password for 'https://EvanS-Dock6@github.com':
-Enumerating objects: 34, done.
-Counting objects: 100% (34/34), done.
-Delta compression using up to 128 threads
-Compressing objects: 100% (21/21), done.
-Writing objects: 100% (22/22), 2.96 KiB | 2.96 MiB/s, done.
-Total 22 (delta 17), reused 0 (delta 0), pack-reused 0
-remote: Resolving deltas: 100% (17/17), completed with 11 local objects.
-To https://github.com/EvanS-Dock6/dock6.git
-ce698b4..5f99310b  alpha_branch -> alpha_branch
-(base) [ehspector@milan2 alpha_branch]$ docs
--bash: docs: command not found
-(base) [ehspector@milan2 alpha_branch]$ cd docs
-(base) [ehspector@milan2 docs]$ ls
-bugfixes610  bugfixes65    dock6_manual.html  new_in_6.11.txt  new_in_6.4.txt  README
-bugfixes611  bugfixes66    faq                new_in_6.12.txt  new_in_6.5.txt  tutorials
-bugfixes612  bugfixes67    faq.htm            new_in_6.13.txt  new_in_6.6.txt
-bugfixes62   bugfixes68    images             new_in_6.1.txt   new_in_6.7.txt
-bugfixes63   bugfixes69    index.htm          new_in_6.2.txt   new_in_6.8.txt
-bugfixes64   bugfixes.htm  new_in_6.10.txt    new_in_6.3.txt   new_in_6.9.txt
-(base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
-(base) [ehspector@milan2 docs]$ home
-(base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/
-(base) [ehspector@milan2 gas_teiger]$ vi gas.in
-(base) [ehspector@milan2 gas_teiger]$ home
-(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs
-(base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
-(base) [ehspector@milan2 docs]$ vi dock6_manual.html
-(base) [ehspector@milan2 docs]$ pwd
-/gpfs/projects/rizzo/espector/builds/alpha_branch/docs
-(base) [ehspector@milan2 docs]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+You can now close your current session on Chimera by going to File >> Close Session
-. Duo Push to XXX-XXX-9204
+=== Preparing the Ligand ===
-Passcode or option (1-1): 1
+Now that we have a ligand only PDB, lets go ahead and generate the two mol2 files with the ligand.
-Pushed a login request to your device...
+The first step is to go to open the <code> 1O86_ligand.pdb </code> on chimera.
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ home
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ cd ..
-(base) [ehspector@milan2 rizzo]$ class
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@milan2 AMS_536]$ cd class_work/
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
-w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi 2w26.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphere_selector 2w26.sph ../001_structure/2w26_ligand_hydrogens_charges.mol2 10.0
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 003
--bash: cd: 003: No such file or directory
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 002
--bash: cd: 002: No such file or directory
-(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh  showbox.in
-(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
- automatically construct box to enclose spheres [Y/N]?
- extra margin to also be enclosed (angstroms)?
-   (this will be added in all 6 directions)
- sphere file-
- cluster number-
-At line 61 of file showbox.f (unit = 1)
-Fortran runtime error: Cannot open file '../002_spheres/selected_spheres.sph': No such file or directory
-Error termination. Backtrace:
+Go to File >> Save Mol2
-#0  0x7ffff7d54ca5 in already_open
-	at ../../../libgfortran/io/open.c:742
-#1  0x4015d9 in ???
-#2  0x40115c in ???
-#3  0x7ffff742958f in ???
-#4  0x7ffff742963f in ???
-#5  0x401194 in ???
-#6  0xffffffffffffffff in ???
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh  showbox.in
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 003
--bash: cd: 003: No such file or directory
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh  showbox.in
-(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
-showbox.sh: line 3: syntax error near unexpected token `&'
-showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < &showbox.in&'
-(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
-showbox.sh: line 3: syntax error near unexpected token `&'
-showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < showbox.in > &showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi 2w26.box.pdb
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ tar -cvf 2w26
-tar: Cowardly refusing to create an empty archive
-Try 'tar --help' or 'tar --usage' for more information.
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  class_work
-(base) [ehspector@milan2 AMS_536]$ cd class_
--bash: cd: class_: No such file or directory
-(base) [ehspector@milan2 AMS_536]$ cd class_work/
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
-w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi grid.
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi grid.out
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi grid.out
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
-w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
-(base) [ehspector@milan2 001_structure]$ vi 2w26_protein_with_charges.mol2
-(base) [ehspector@milan2 001_structure]$ pwd
-/gpfs/home/ehspector/AMS_536/class_work/001_structure
-(base) [ehspector@milan2 001_structure]$ homw
--bash: homw: command not found
-(base) [ehspector@milan2 001_structure]$ home
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ cd gas_test/
-(base) [ehspector@milan2 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@milan2 gas_test]$ cd ..
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ cd gas_test/
-(base) [ehspector@milan2 gas_test]$ vi test.in
-(base) [ehspector@milan2 gas_test]$ vi test_2.in
-(base) [ehspector@milan2 gas_test]$ cd gas_f_test/
-(base) [ehspector@milan2 gas_f_test]$ ls
-diff.out   gas_0.out_scored.mol2  gas_1.out              gas_50.in   gas_50.out_scored.mol2
-gas_0.out  gas_1.in               gas_1.out_scored.mol2  gas_50.out
-(base) [ehspector@milan2 gas_f_test]$ vi gas_1.in
-(base) [ehspector@milan2 gas_f_test]$ cd ..
-(base) [ehspector@milan2 gas_test]$ cd ..
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ cd gas_test/
-(base) [ehspector@milan2 gas_test]$ ls
-s0v_GA.in                       4s0v_GA_output.restart0028.mol2
-s0v_GA.out                      4s0v_GA_output.restart0029.mol2
-s0v_GA_output.restart0000.mol2  4s0v_GA_output.restart0030.mol2
-s0v_GA_output.restart0001.mol2  4s0v_GA_output.restart0031.mol2
-s0v_GA_output.restart0002.mol2  4s0v_GA_output.restart0032.mol2
-s0v_GA_output.restart0003.mol2  4s0v_GA_output.restart0033.mol2
-s0v_GA_output.restart0004.mol2  4s0v_GA_output.restart0034.mol2
-s0v_GA_output.restart0005.mol2  4s0v_GA_output.restart0035.mol2
-s0v_GA_output.restart0006.mol2  4s0v_GA_output.restart0036.mol2
-s0v_GA_output.restart0007.mol2  4s0v_GA_output.restart0037.mol2
-s0v_GA_output.restart0008.mol2  4s0v_GA_output.restart0038.mol2
-s0v_GA_output.restart0009.mol2  4s0v_GA_output.restart0039.mol2
-s0v_GA_output.restart0010.mol2  4s0v_GA_output.restart0040.mol2
-s0v_GA_output.restart0011.mol2  4s0v_GA_output.restart0041.mol2
-s0v_GA_output.restart0012.mol2  4s0v_GA_output.restart0042.mol2
-s0v_GA_output.restart0013.mol2  4s0v_GA_output.restart0043.mol2
-s0v_GA_output.restart0014.mol2  4s0v_GA_output.restart0044.mol2
-s0v_GA_output.restart0015.mol2  4s0v_GA_output.restart0045.mol2
-s0v_GA_output.restart0016.mol2  4s0v_GA_output.restart0046.mol2
-s0v_GA_output.restart0017.mol2  4s0v_GA_output.restart0047.mol2
-s0v_GA_output.restart0018.mol2  4s0v_GA_output.restart0048.mol2
-s0v_GA_output.restart0019.mol2  4s0v_GA_output.restart0049.mol2
-s0v_GA_output.restart0020.mol2  4s0v_GA_output.restart0050.mol2
-s0v_GA_output.restart0021.mol2  4s0v_GA.slurm
-s0v_GA_output.restart0022.mol2  charge_data
-s0v_GA_output.restart0023.mol2  gas_f_test
-s0v_GA_output.restart0024.mol2  gas_RD_Test
-s0v_GA_output.restart0025.mol2  GA.txt
-s0v_GA_output.restart0026.mol2  test_2.in
-s0v_GA_output.restart0027.mol2  test.in
-(base) [ehspector@milan2 gas_test]$ cd gas_f_test/
-(base) [ehspector@milan2 gas_f_test]$ ls
-diff.out   gas_0.out_scored.mol2  gas_1.out              gas_50.in   gas_50.out_scored.mol2
-gas_0.out  gas_1.in               gas_1.out_scored.mol2  gas_50.out
-(base) [ehspector@milan2 gas_f_test]$ cp gas_1.in gas_2.in
-(base) [ehspector@milan2 gas_f_test]$ vi gas_2.in
-(base) [ehspector@milan2 gas_f_test]$ vi gas_2.in
-(base) [ehspector@milan2 gas_f_test]$ dock6 -i gas_2.in -o gas_2.out
-^C
-(base) [ehspector@milan2 gas_f_test]$ ls
-diff.out               gas_1.in               gas_2.in   gas_50.out
-gas_0.out              gas_1.out              gas_2.out  gas_50.out_scored.mol2
-gas_0.out_scored.mol2  gas_1.out_scored.mol2  gas_50.in  gas.out_scored.mol2
-(base) [ehspector@milan2 gas_f_test]$ vi gas_2.out
-(base) [ehspector@milan2 gas_f_test]$ home
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs/
-(base) [ehspector@milan2 docs]$ ls
-bugfixes610  bugfixes65    dock6_manual.html  new_in_6.11.txt  new_in_6.4.txt  README
-bugfixes611  bugfixes66    faq                new_in_6.12.txt  new_in_6.5.txt  tutorials
-bugfixes612  bugfixes67    faq.htm            new_in_6.13.txt  new_in_6.6.txt
-bugfixes62   bugfixes68    images             new_in_6.1.txt   new_in_6.7.txt
-bugfixes63   bugfixes69    index.htm          new_in_6.2.txt   new_in_6.8.txt
-bugfixes64   bugfixes.htm  new_in_6.10.txt    new_in_6.3.txt   new_in_6.9.txt
-(base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
-(base) [ehspector@milan2 docs]$ class
-(base) [ehspector@milan2 AMS_536]$ mkdir 1086 5EEN
-(base) [ehspector@milan2 AMS_536]$ ls
-  5EEN  class_project  class_work
-(base) [ehspector@milan2 AMS_536]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Spring_25 % cd AMS_536/Tutorial
-(base) supremestudier@Evans-MBP Tutorial % ls
-w26.box.pdb
-w26.pdb
-w26.pdb1.gz
-w26.sph
-w26_charges.pdb
-w26_ligand.pdb
-w26_ligand_hydrogens_charges.mol2
-w26_ligand_hydrogens_charges.pdb
-w26_ligand_no_hydrogens_no_charges.mol2
-w26_new_surface.dms
-w26_protein_no_hydrogens_no_charges.mol2
-w26_protein_only.pdb
-w26_protein_with_charges.mol2
-w26_surface.dms
-selected_spheres.sph
-(base) supremestudier@Evans-MBP Tutorial % vi 2w26.pdb
-(base) supremestudier@Evans-MBP Tutorial % ls
-w26.box.pdb
-w26.pdb
-w26.pdb1.gz
-w26.sph
-w26_charges.pdb
-w26_ligand.pdb
-w26_ligand_hydrogens_charges.mol2
-w26_ligand_hydrogens_charges.pdb
-w26_ligand_no_hydrogens_no_charges.mol2
-w26_new_surface.dms
-w26_protein_no_hydrogens_no_charges.mol2
-w26_protein_only.pdb
-w26_protein_with_charges.mol2
-w26_surface.dms
-selected_spheres.sph
-(base) supremestudier@Evans-MBP Tutorial % mdkir 2w26
-zsh: command not found: mdkir
-(base) supremestudier@Evans-MBP Tutorial % mkdir 2w26
-(base) supremestudier@Evans-MBP Tutorial % ls
-w26
-w26.box.pdb
-w26.pdb
-w26.pdb1.gz
-w26.sph
-w26_charges.pdb
-w26_ligand.pdb
-w26_ligand_hydrogens_charges.mol2
-w26_ligand_hydrogens_charges.pdb
-w26_ligand_no_hydrogens_no_charges.mol2
-w26_new_surface.dms
-w26_protein_no_hydrogens_no_charges.mol2
-w26_protein_only.pdb
-w26_protein_with_charges.mol2
-w26_surface.dms
-selected_spheres.sph
-(base) supremestudier@Evans-MBP Tutorial % cd ..
-(base) supremestudier@Evans-MBP AMS_536 % cd ..
-(base) supremestudier@Evans-MBP Spring_25 % cd AMS_548
-(base) supremestudier@Evans-MBP AMS_548 % ls
-Polaris.ipynb				ligand_poses_reference_structures.zip
-ligand_poses_reference_structures
-(base) supremestudier@Evans-MBP AMS_548 % pwd
-/Users/supremestudier/Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_548
-(base) supremestudier@Evans-MBP AMS_548 % pip install pymol
-ERROR: Could not find a version that satisfies the requirement pymol (from versions: none)
-ERROR: No matching distribution found for pymol
-(base) supremestudier@Evans-MBP AMS_548 % which python
-/Users/supremestudier/anaconda3/bin/python
-(base) supremestudier@Evans-MBP AMS_548 % tar -jxf pymol-X_XX-bin-linux-x86-glibc23.tar.bz2
-tar: Error opening archive: Failed to open 'pymol-X_XX-bin-linux-x86-glibc23.tar.bz2'
-(base) supremestudier@Evans-MBP AMS_548 % conda install -c conda-forge -c schrodinger pymol-bundle
-Retrieving notices: ...working... done
-Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
-done
-Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
-Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
-Collecting package metadata (repodata.json): / WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
-WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
-WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
-done
-Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
-CondaError: KeyboardInterrupt
+Lets give the title of this first mol2 to denote no hydrogens or charge on the ligand.
+Call it <code> 1O86_ligand_nH_ncH.mol2 </code>
-(base) supremestudier@Evans-MBP AMS_548 %
-(base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U
-Collecting boltz
-  Obtaining dependency information for boltz from https://files.pythonhosted.org/packages/22/b3/6bbc7aaea024d3dc13abc8e94ee32df74dd63bfc016e0f87abd20d0dcbbd/boltz-0.4.1-py3-none-any.whl.metadata
-  Downloading boltz-0.4.1-py3-none-any.whl.metadata (4.8 kB)
-Collecting torch>=2.2 (from boltz)
-  Obtaining dependency information for torch>=2.2 from https://files.pythonhosted.org/packages/3f/14/e105b8ef6d324e789c1589e95cb0ab63f3e07c2216d68b1178b7c21b7d2a/torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl.metadata
-  Downloading torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl.metadata (25 kB)
-Collecting numpy==1.26.3 (from boltz)
-  Obtaining dependency information for numpy==1.26.3 from https://files.pythonhosted.org/packages/42/db/82cc805d96ba48622fbb7395a7b44cf59567fca235e397cdf64555081773/numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata
-  Downloading numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (61 kB)
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-Collecting hydra-core==1.3.2 (from boltz)
-  Obtaining dependency information for hydra-core==1.3.2 from https://files.pythonhosted.org/packages/c6/50/e0edd38dcd63fb26a8547f13d28f7a008bc4a3fd4eb4ff030673f22ad41a/hydra_core-1.3.2-py3-none-any.whl.metadata
-  Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
-Collecting pytorch-lightning==2.4.0 (from boltz)
-  Obtaining dependency information for pytorch-lightning==2.4.0 from https://files.pythonhosted.org/packages/2b/d2/ecd65ff1e0b1ca79f9785dd65d5ced7ec2643a828068aaa24e47e4c84a14/pytorch_lightning-2.4.0-py3-none-any.whl.metadata
-  Downloading pytorch_lightning-2.4.0-py3-none-any.whl.metadata (21 kB)
-Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
-Collecting dm-tree==0.1.8 (from boltz)
-  Obtaining dependency information for dm-tree==0.1.8 from https://files.pythonhosted.org/packages/b1/65/4f10a68dde5fa0c91043c9c899e9bc79b1657ba932d39a5f8525c0058e68/dm_tree-0.1.8-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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-Collecting requests==2.32.3 (from boltz)
-  Obtaining dependency information for requests==2.32.3 from https://files.pythonhosted.org/packages/f9/9b/335f9764261e915ed497fcdeb11df5dfd6f7bf257d4a6a2a686d80da4d54/requests-2.32.3-py3-none-any.whl.metadata
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-Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
-Collecting types-requests (from boltz)
-  Obtaining dependency information for types-requests from https://files.pythonhosted.org/packages/d7/01/485b3026ff90e5190b5e24f1711522e06c79f4a56c8f4b95848ac072e20f/types_requests-2.32.0.20241016-py3-none-any.whl.metadata
-  Downloading types_requests-2.32.0.20241016-py3-none-any.whl.metadata (1.9 kB)
-Collecting einops==0.8.0 (from boltz)
-  Obtaining dependency information for einops==0.8.0 from https://files.pythonhosted.org/packages/44/5a/f0b9ad6c0a9017e62d4735daaeb11ba3b6c009d69a26141b258cd37b5588/einops-0.8.0-py3-none-any.whl.metadata
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-Collecting einx==0.3.0 (from boltz)
-  Obtaining dependency information for einx==0.3.0 from https://files.pythonhosted.org/packages/90/04/4a730d74fd908daad86d6b313f235cdf8e0cf1c255b392b7174ff63ea81a/einx-0.3.0-py3-none-any.whl.metadata
-  Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)
-Collecting fairscale==0.4.13 (from boltz)
-  Downloading fairscale-0.4.13.tar.gz (266 kB)
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-  Installing build dependencies ... done
-  Getting requirements to build wheel ... done
-  Installing backend dependencies ... done
-  Preparing metadata (pyproject.toml) ... done
-Collecting mashumaro==3.14 (from boltz)
-  Obtaining dependency information for mashumaro==3.14 from https://files.pythonhosted.org/packages/1b/35/8d63733a2c12149d0c7663c29bf626bdbeea5f0ff963afe58a42b4810981/mashumaro-3.14-py3-none-any.whl.metadata
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-Collecting modelcif==1.2 (from boltz)
-  Downloading modelcif-1.2.tar.gz (66 kB)
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-  Preparing metadata (setup.py) ... done
-Collecting wandb==0.18.7 (from boltz)
-  Obtaining dependency information for wandb==0.18.7 from https://files.pythonhosted.org/packages/0c/6d/cf600f649090d3c3f8ac86becf10a1d3d5c1ce305389c4d02cc9488fb8d0/wandb-0.18.7-py3-none-macosx_10_13_x86_64.whl.metadata
-  Downloading wandb-0.18.7-py3-none-macosx_10_13_x86_64.whl.metadata (9.7 kB)
-Collecting click==8.1.7 (from boltz)
-  Obtaining dependency information for click==8.1.7 from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata
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-Collecting pyyaml==6.0.2 (from boltz)
-  Obtaining dependency information for pyyaml==6.0.2 from https://files.pythonhosted.org/packages/f8/aa/7af4e81f7acba21a4c6be026da38fd2b872ca46226673c89a758ebdc4fd2/PyYAML-6.0.2-cp311-cp311-macosx_10_9_x86_64.whl.metadata
-  Downloading PyYAML-6.0.2-cp311-cp311-macosx_10_9_x86_64.whl.metadata (2.1 kB)
-Collecting biopython==1.84 (from boltz)
-  Obtaining dependency information for biopython==1.84 from https://files.pythonhosted.org/packages/c5/7b/c1e9f66e23b01958ae0284a437a0e586ce20387fc6ea0382c21230ac59bc/biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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-Collecting scipy==1.13.1 (from boltz)
-  Obtaining dependency information for scipy==1.13.1 from https://files.pythonhosted.org/packages/b4/15/4a4bb1b15bbd2cd2786c4f46e76b871b28799b67891f23f455323a0cdcfb/scipy-1.13.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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-Collecting frozendict (from einx==0.3.0->boltz)
-  Obtaining dependency information for frozendict from https://files.pythonhosted.org/packages/04/13/d9839089b900fa7b479cce495d62110cddc4bd5630a04d8469916c0e79c5/frozendict-2.4.6-py311-none-any.whl.metadata
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-Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz)
-  Obtaining dependency information for omegaconf<2.4,>=2.2 from https://files.pythonhosted.org/packages/e3/94/1843518e420fa3ed6919835845df698c7e27e183cb997394e4a670973a65/omegaconf-2.3.0-py3-none-any.whl.metadata
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-Collecting antlr4-python3-runtime==4.9.* (from hydra-core==1.3.2->boltz)
-  Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
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-  Preparing metadata (setup.py) ... done
-Requirement already satisfied: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
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-Collecting ihm>=1.7 (from modelcif==1.2->boltz)
-  Downloading ihm-1.8.tar.gz (350 kB)
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-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)
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-Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz)
-  Obtaining dependency information for torchmetrics>=0.7.0 from https://files.pythonhosted.org/packages/9d/e1/84066ff60a20dfa63f4d9d8ddc280d5ed323b7f06504dbb51c523b690116/torchmetrics-1.6.1-py3-none-any.whl.metadata
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-  Obtaining dependency information for lightning-utilities>=0.10.0 from https://files.pythonhosted.org/packages/50/8d/da77ceb92ed674da93959184a2777d08ccbd872559fb52aba16b91686b7e/lightning_utilities-0.12.0-py3-none-any.whl.metadata
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-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)
+'''Running Dock Prep'''
-Collecting pip
-  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/85/8a/1ddf40be20103bcc605db840e9ade09c8e8c9f920a03e9cfe88eae97a058/pip-25.0-py3-none-any.whl.metadata
-  Downloading pip-25.0-py3-none-any.whl.metadata (3.7 kB)
-Downloading pip-25.0-py3-none-any.whl (1.8 MB)
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-Installing collected packages: pip
-  Attempting uninstall: pip
-    Found existing installation: pip 23.2.1
-    Uninstalling pip-23.2.1:
-      Successfully uninstalled pip-23.2.1
-Successfully installed pip-25.0
-(base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U
-Requirement already satisfied: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1)
-Requirement already satisfied: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2)
-Requirement already satisfied: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3)
-Requirement already satisfied: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2)
-Requirement already satisfied: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0)
-Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
-Requirement already satisfied: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8)
-Requirement already satisfied: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3)
-Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
-Requirement already satisfied: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016)
-Requirement already satisfied: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0)
-Requirement already satisfied: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0)
-Requirement already satisfied: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13)
-Requirement already satisfied: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14)
-Requirement already satisfied: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2)
-Requirement already satisfied: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7)
-Requirement already satisfied: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7)
-Requirement already satisfied: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2)
-Requirement already satisfied: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84)
-Requirement already satisfied: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1)
-Requirement already satisfied: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (1.11.1)
-Requirement already satisfied: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6)
-Requirement already satisfied: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0)
-Requirement already satisfied: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3)
-Requirement already satisfied: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
-Requirement already satisfied: typing-extensions>=4.1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from mashumaro==3.14->boltz) (4.12.2)
-Requirement already satisfied: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8)
-Requirement already satisfied: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
-Requirement already satisfied: fsspec>=2022.5.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (2024.12.0)
-Requirement already satisfied: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1)
-Requirement already satisfied: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0)
-Requirement already satisfied: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
-Requirement already satisfied: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
-Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0)
-Requirement already satisfied: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
-Requirement already satisfied: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0)
-Requirement already satisfied: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44)
-Requirement already satisfied: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
-Requirement already satisfied: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
-Requirement already satisfied: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
-Requirement already satisfied: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0)
-Requirement already satisfied: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4)
-Requirement already satisfied: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
-Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
-Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
-Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
-Requirement already satisfied: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
-Requirement already satisfied: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
-Requirement already satisfied: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
-Requirement already satisfied: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
-Requirement already satisfied: six>=1.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz) (1.16.0)
-Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (3.8.5)
-Requirement already satisfied: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12)
-Requirement already satisfied: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
-Requirement already satisfied: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
-Requirement already satisfied: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->einx==0.3.0->boltz) (1.3.0)
-Requirement already satisfied: attrs>=17.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (22.1.0)
-Requirement already satisfied: multidict<7.0,>=4.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (6.0.2)
-Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (4.0.2)
-Requirement already satisfied: yarl<2.0,>=1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.8.1)
-Requirement already satisfied: frozenlist>=1.1.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.3.3)
-Requirement already satisfied: aiosignal>=1.1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.2.0)
-Requirement already satisfied: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2)
-(base) supremestudier@Evans-MBP AMS_548 % pip check
-tables 3.8.0 requires blosc2, which is not installed.
-tables 3.8.0 requires cython, which is not installed.
-conda-repo-cli 1.0.75 requires requests-mock, which is not installed.
-spyder 5.4.3 requires pyqt5, which is not installed.
-spyder 5.4.3 requires pyqtwebengine, which is not installed.
-gensim 4.3.0 requires fuzzytm, which is not installed.
-conda-repo-cli 1.0.75 has requirement clyent==1.2.1, but you have clyent 1.2.2.
-conda-repo-cli 1.0.75 has requirement PyYAML==6.0.1, but you have pyyaml 6.0.2.
-conda-repo-cli 1.0.75 has requirement requests==2.31.0, but you have requests 2.32.3.
-numba 0.57.0 has requirement numpy<1.25,>=1.21, but you have numpy 1.26.3.
-python-lsp-black 1.2.1 has requirement black>=22.3.0, but you have black 0.0.
-anaconda-cloud-auth 0.1.3 has requirement pydantic<2.0, but you have pydantic 2.10.6.
-s3fs 2023.4.0 has requirement fsspec==2023.4.0, but you have fsspec 2024.12.0.
-aiobotocore 2.5.0 has requirement botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99.
-conda-verify 3.4.2 is not supported on this platform
-(base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U --use-deprecated=legacy-resolver
-Requirement already up-to-date: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1)
-Requirement already satisfied, skipping upgrade: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2)
-Requirement already satisfied, skipping upgrade: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3)
-Requirement already satisfied, skipping upgrade: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2)
-Requirement already satisfied, skipping upgrade: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0)
-Requirement already satisfied, skipping upgrade: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
-Requirement already satisfied, skipping upgrade: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8)
-Requirement already satisfied, skipping upgrade: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3)
-Requirement already satisfied, skipping upgrade: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
-Requirement already satisfied, skipping upgrade: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016)
-Requirement already satisfied, skipping upgrade: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0)
-Requirement already satisfied, skipping upgrade: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0)
-Requirement already satisfied, skipping upgrade: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13)
-Requirement already satisfied, skipping upgrade: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14)
-Requirement already satisfied, skipping upgrade: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2)
-Requirement already satisfied, skipping upgrade: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7)
-Requirement already satisfied, skipping upgrade: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7)
-Requirement already satisfied, skipping upgrade: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2)
-Requirement already satisfied, skipping upgrade: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84)
-Requirement already satisfied, skipping upgrade: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1)
-Requirement already satisfied, skipping upgrade: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
-Requirement already satisfied, skipping upgrade: typing-extensions>=4.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (4.12.2)
-Requirement already satisfied, skipping upgrade: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (1.11.1)
-Requirement already satisfied, skipping upgrade: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
-Requirement already satisfied, skipping upgrade: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
-Requirement already satisfied, skipping upgrade: fsspec in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (2024.12.0)
-Requirement already satisfied, skipping upgrade: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0)
-Requirement already satisfied, skipping upgrade: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3)
-Requirement already satisfied, skipping upgrade: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
-Requirement already satisfied, skipping upgrade: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
-Requirement already satisfied, skipping upgrade: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1)
-Requirement already satisfied, skipping upgrade: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0)
-Requirement already satisfied, skipping upgrade: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
-Requirement already satisfied, skipping upgrade: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
-Requirement already satisfied, skipping upgrade: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
-Requirement already satisfied, skipping upgrade: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0)
-Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
-Requirement already satisfied, skipping upgrade: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
-Requirement already satisfied, skipping upgrade: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
-Requirement already satisfied, skipping upgrade: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
-Requirement already satisfied, skipping upgrade: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6)
-Requirement already satisfied, skipping upgrade: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8)
-Requirement already satisfied, skipping upgrade: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0)
-Requirement already satisfied, skipping upgrade: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44)
-Requirement already satisfied, skipping upgrade: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
-Requirement already satisfied, skipping upgrade: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0; sys_platform != "linux" in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
-Requirement already satisfied, skipping upgrade: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
-Requirement already satisfied, skipping upgrade: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0)
-Requirement already satisfied, skipping upgrade: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4)
-Requirement already satisfied, skipping upgrade: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
-Requirement already satisfied, skipping upgrade: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->torch>=2.2->boltz) (1.3.0)
-Requirement already satisfied, skipping upgrade: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
-Requirement already satisfied, skipping upgrade: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas>=2.2.2->boltz) (1.16.0)
-Requirement already satisfied, skipping upgrade: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
-Requirement already satisfied, skipping upgrade: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12)
-Requirement already satisfied, skipping upgrade: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2)
-(base) supremestudier@Evans-MBP AMS_548 % conda activate
-(base) supremestudier@Evans-MBP AMS_548 % conda env list
-# conda environments:
-#
-base                  *  /Users/supremestudier/anaconda3
-sage-dev                 /Users/supremestudier/anaconda3/envs/sage-dev
-                         /Users/supremestudier/opt/anaconda3
-(base) supremestudier@Evans-MBP AMS_548 % which boltz
+To generate the second mol2 you are more than welcome to revisit the steps taken to generate the second
-/Users/supremestudier/anaconda3/bin/boltz
+protein mol2. In the case of the ligand, we will introduce an alternative with a program called Dock Prep.
-(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:
+First, return to <code> 1O86_ligand.pdb </code> on chimera:
-. Duo Push to XXX-XXX-9204
+Go to Tools >> Structure Editing >> DockPrep
-Passcode or option (1-1): 1
+The following pop-up menu will appear:
-Pushed a login request to your device...
+[[File:dock_prep.png|600px]]
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ home
-(base) [ehspector@milan1 espector]$ cd 4s0v/
-(base) [ehspector@milan1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@milan1 gas_teiger]$ cd no_charge/
-(base) [ehspector@milan1 no_charge]$ ls
-s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
-s0v.lig_no_charge.min_scored.mol2     gas_2.out
-s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
-(base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2
-(base) [ehspector@milan1 no_charge]$ ls
-s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
-s0v.lig_no_charge.min_scored.mol2     gas_2.out
-s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
-(base) [ehspector@milan1 no_charge]$ cd ..
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@milan1 gas_teiger]$ vi gas.in
-(base) [ehspector@milan1 gas_teiger]$ cd ..
-(base) [ehspector@milan1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@milan1 4s0v]$ cd energy_min/
-(base) [ehspector@milan1 energy_min]$ ls
-s0v.lig.min_scored.mol2  min.in  min.out
-(base) [ehspector@milan1 energy_min]$ vi 4s0v.lig.min_scored.mol2
-(base) [ehspector@milan1 energy_min]$ cd ..
-(base) [ehspector@milan1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out
-(base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@milan1 gas_teiger]$ cd no_charge/
-(base) [ehspector@milan1 no_charge]$ ls
-s0v_ligand_hydrogens_no_charges.mol2  gas_2.in
-s0v.lig_no_charge.min_scored.mol2     gas_2.out
-s0v_no_hydrogens_no_charges.mol2      gas.out_scored.mol2
-(base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2
-(base) [ehspector@milan1 no_charge]$ cd ..
-(base) [ehspector@milan1 gas_teiger]$ cd ..
-(base) [ehspector@milan1 4s0v]$ vi  energy_min/4s0v.lig.min_scored.mol2
-(base) [ehspector@milan1 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/test.mol2
-(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas.out  no_charge            no_gas.out  test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi test.mol2
-(base) [ehspector@milan1 gas_teiger]$ cp gas.in gas_2.in
-(base) [ehspector@milan1 gas_teiger]$ pwd
-/gpfs/projects/rizzo/espector/4s0v/gas_teiger
-(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
-(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
-(base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas_2.in   gas.in   gas.out_scored.mol2  no_gas.in   no_gas.out_scored.mol2
-gas_2.out  gas.out  no_charge            no_gas.out  test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas_2.out
-(base) [ehspector@milan1 gas_teiger]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+All of the default parameters are sufficient. Select OK.
-. Duo Push to XXX-XXX-9204
+The next set of drop down menus will be the same as adding hydrogens and charges to a protein.
-Passcode or option (1-1): 1
+'''Remember''' all of the defaults are okay for adding hydrogens, but make sure you switch from
-Pushed a login request to your device...
+AM1-BCC to Gasteiger charges when adding the charges for the ligand.
-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:
+All other defaults are sufficient for each of the other pop-up menus.
-. Duo Push to XXX-XXX-9204
+The following images show the pop-up menus that will appear after you accept using Dock Prep and contain the acceptable defaults:
-Passcode or option (1-1): 1
+[[File:Lh_menu.png|600px]]
-Pushed a login request to your device...
+The Hydrogen Menu
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ ls
-  5EEN  class_project  class_work
-(base) [ehspector@milan2 AMS_536]$ cd class_
--bash: cd: class_: No such file or directory
-(base) [ehspector@milan2 AMS_536]$ cd class_work/
-(base) [ehspector@milan2 class_work]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 class_work]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ mkdir Tutorials
-(base) [ehspector@milan2 AMS_536]$ mv class_work/ Tutorials/
-(base) [ehspector@milan2 AMS_536]$ ls
-  5EEN  class_project  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-class_work
-(base) [ehspector@milan2 Tutorials]$ mv class_work/ 2w26
-(base) [ehspector@milan2 Tutorials]$ ls
-w26
-(base) [ehspector@milan2 Tutorials]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ mv 1086/ 5EEN/ Tutorials/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 2w26]$ cd 001
--bash: cd: 001: No such file or directory
-(base) [ehspector@milan2 2w26]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-w26_ligand_hydrogens_charges.mol2        2w26_protein_no_hydrogens_no_charges.mol2
-w26_ligand_no_hydrogens_no_charges.mol2  2w26_protein_with_charges.mol2
-(base) [ehspector@milan2 001_structure]$ rm *.mol2
-(base) [ehspector@milan2 001_structure]$ ls
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_new_surface.dms  2w26.sph  INSPH  OUTSPH  selected_spheres.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm selected_spheres.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_new_surface.dms
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-INSPH  OUTSPH  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-INSPH  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-showbox.sh   2w26.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ rm 2w26.box.pdb
-(base) [ehspector@milan2 003_gridbox]$ rm grid.out
-(base) [ehspector@milan2 003_gridbox]$ mv 01showbox.sh showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
- grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 2w26]$ cd 004_dock/
-(base) [ehspector@milan2 004_dock]$ ls
-(base) [ehspector@milan2 004_dock]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 5EEN/commands.txt
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/
-(base) [ehspector@milan2 5EEN]$ ls
-commands.txt
-(base) [ehspector@milan2 5EEN]$ bash commands.txt
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 5EEN]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+[[File:Lch_menu.png|600px]]
-. Duo Push to XXX-XXX-9204
+The Charge Menu
-Passcode or option (1-1): 1
+[[File:LncH.png|600px]]
-Pushed a login request to your device...
+The Net Charge Menu
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/001_structure/
-(base) [ehspector@milan1 001_structure]$ pwd
-/gpfs/home/ehspector/AMS_536/Tutorials/5EEN/001_structure
-(base) [ehspector@milan1 001_structure]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd 001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een_surface.dms
-(base) [ehspector@milan1 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-INSPH  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/002_surface_spheres/sphere.sph 5EEN/002_surface_spheres/sphere.sph
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een_surface.dms  INSPH  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph
+What's neat about Dock Prep is that the last pop-up menu will be the Save Mol2 menu:
-Press ENTER or type command to continue
+[[File:mol2_menu.png|600px]]
-(base) [ehspector@milan1 002_surface_spheres]$ bash sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een.sph  5een_surface.dms  INSPH  OUTSPH  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 5EEN]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een.sph  5een_surface.dms  INSPH  OUTSPH  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-INSPH  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een.sph  5een_surface.dms  INSPH  OUTSPH  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd 001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ bash selected_sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een.sph          INSPH   selected_sphere.sph   sphere.sph
-een_surface.dms  OUTSPH  selected_spheres.sph
-(base) [ehspector@milan1 002_surface_spheres]$ mv selected_sphere.sph select.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi selected_spheres.sph
-(base) [ehspector@milan1 002_surface_spheres]$ cd ..
-(base) [ehspector@milan1 5EEN]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan1 5EEN]$ mv 004_dock/ 004_energymin
-(base) [ehspector@milan1 5EEN]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ ls
- grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/showbox.sh 5EEN/003_gridbox/showbox.sh
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/
-(base) [ehspector@milan1 5EEN]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ ls
-showbox.in  showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ vi showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ bash showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ vi grid.in
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   grid.in   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ rm grid.in
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ ls
- grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ vi grid.in
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.in 5EEN/003_gridbox/grid.in
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.sh 5EEN/003_gridbox/grid.sh
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd 001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ vi grid.
-(base) [ehspector@milan1 003_gridbox]$ vi grid.in
-(base) [ehspector@milan1 003_gridbox]$ vi grid.in
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ vi grid.in
-(base) [ehspector@milan1 003_gridbox]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan1 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan1 003_gridbox]$ bash grid.sh
-(base) [ehspector@milan1 003_gridbox]$ ls
-een.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
- grid.bmp       grid.nrg   grid.sh   '&showbox.log&'
-(base) [ehspector@milan1 003_gridbox]$ vi grid.out
-(base) [ehspector@milan1 003_gridbox]$ cd ../004_energymin/
-(base) [ehspector@milan1 004_energymin]$ ls
-(base) [ehspector@milan1 004_energymin]$ touch min.in
-(base) [ehspector@milan1 004_energymin]$ ls
-min.in
-(base) [ehspector@milan1 004_energymin]$ dock6 -i min.in
+Lets give this mol2 a file name that specifies that it has hydrogens and charges.
+Call it <code> 1O86_ligand_wH_wcH.mol2 </code>
---------------------------------------
+Congratulations, you've generated all the necessary mol2 files to advance to the next steps of this tutorial.
-DOCK v6.12
-Released April 2024
+Lets transfer the mol2 files onto seawulf using the following command
-Copyright UCSF
---------------------------------------
+   scp *mol2 yourusername@stonybrook.edu:'/gpfs/home/yourusername/tutorial/001_structure'
-Conformational Sampling Parameters
+== 002: Spheres ==
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
-Internal Energy Parameters
+=== Generate the Required Surface File ===
-------------------------------------------------------------------------------------------
-                                          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
+# Open the <code>1O86_protein_nH_ncH.mol2</code> (with no hydrogens, no charges) in Chimera and hit Actions >> Surface >> Show
-------------------------------------------------------------------------------------------
+# Write the DMS file by choosing Tools > Structure Editing > Write DMS; save the file as <code>1O86.dms</code>
-                                             ligand_atom_file [database.mol2] ():../001_structure/5een_ligand_H_cH.mol2
+# Upload the DMS file to your <code>~/tutorial/002_spheres</code> directory on Seawulf using <code>scp</code>
-                                            limit_max_ligands [no] (yes no):
+# Now, move to the Seawulf terminal interface and navigate to your <code>~/tutorial/002_spheres</code> directory. Create a sphgen input file using the following command:
-                                                skip_molecule [no] (yes no):
+ vi INSPH
-                                           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
+:5. Paste the following into your input file, ensuring that no additional lines are pasted:
-------------------------------------------------------------------------------------------
+ ./1O86.dms
-                                          use_database_filter [no] (yes no):no
+ R
+ X
+.0
+.0
+.4
+O86.sph
-Orient Ligand Parameters
+:6. Run the program with the following command
-------------------------------------------------------------------------------------------
-                                                orient_ligand [yes] (yes no):no
-Bump Filter Parameters
+ sphgen -i INSPH -o OUTSPH
-------------------------------------------------------------------------------------------
-                                                  bump_filter [no] (yes no):no
-Master Score Parameters
+:7. Download the output file to your local directory and File >> Open it in the same scene as your protein file in Chimera. This will overlay the generated spheres on the protein.
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):yes
-Contact Score Parameters
+[[File:1O86_allsphereoverlay.png|600px]]
-------------------------------------------------------------------------------------------
-                                        contact_score_primary [no] (yes no):
-Grid Score Parameters
+Based on the overlay the ribbons are aligned with the spheres indicating the generation of surface spheres was successful.
-------------------------------------------------------------------------------------------
-                                           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
+=== Selecting Spheres Localized on Binding Site ===
-------------------------------------------------------------------------------------------
+#Run program on dock 6 called sphere_selector:
+ sphere_selector 1O86.sph ../001_structure/1O86_ligand_nH_ncH.mol2 10.0
+:2. Output file will automatically be written as selected_spheres.sph
+:3. Download this file to your local computer and overlay the file with your original protein file to ensure the spheres are localized over your ligand in the same manner as the 1O86.sph file in the previous step.
+:4. Select and hide binding spheres to ensure they are where the ligand is located
-Dock3.5 Score Parameters
+[[File:1O86_selsphereoverlay.png|600px]]
-------------------------------------------------------------------------------------------
-Continuous Energy Score Parameters
+These spheres will be used for initial orientation of the ligand during docking, and provide a rough approximation of the negative space of the receptor.
-------------------------------------------------------------------------------------------
-Footprint Similarity Score Parameters
+== 003: Grid/box ==
-------------------------------------------------------------------------------------------
-Pharmacophore Similarity Score Parameters
+Generating box and grid. The box and grid generation specify the 3-D space where the docking simulation will take place. The box defines the 3-D space where the docking algorithm will search for binding orientations and conformations of the ligand. The box size should be large enough to include the binding space, but not too large to conserve computational cost. The grid pattern allows for energy calculations between protein and ligand. A smaller grid step would allow for more precise calculations but would be computationally expensive and time consuming. A larger grid step would be computationally cheaper but would be lower in accuracy.
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
+=== Generating the Box ===
-------------------------------------------------------------------------------------------
+Move to your <code>~/tutorial/003_gridbox</code> directory. Create an input file for generating a box around the ligand binding site.
+ vi showbox.in
+Insert the following code into the file. These are parameters for the showbox program:
+ Y
+.0
+ ../002_spheres/selected_spheres.sph
+O86.box.pdb
-Internal Energy Score Parameters
+This will construct a box that will enclose the binding spheres that are localized on the binding side. The box will have dimensions of 8.0 Angstroms from the binding spheres.
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
+Run the input file using the following command:
-------------------------------------------------------------------------------------------
+  showbox < showbox.in
-Zou GB/SA Score Parameters
+An output file titled <code>1O86.box.pdb</code> will be generated in your local directory.
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
+=== Generating the Grid ===
-------------------------------------------------------------------------------------------
-SASA Score Parameters
+ vi grid.in
-------------------------------------------------------------------------------------------
-Amber Score Parameters
+Insert the following into your input file:
-------------------------------------------------------------------------------------------
+ allow_non_integral_charges                no
+ compute_grids                             yes
+ grid_spacing                              0.4
+ output_molecule                           no
+ contact_score                             no
+ energy_score                              yes
+ energy_cutoff_distance                    9999
+ atom_model                                a
+ attractive_exponent                       6
+ repulsive_exponent                        9
+ distance_dielectric                       yes
+ dielectric_factor                         4
+ bump_filter                               yes
+ bump_overlap                              0.75
+ receptor_file                             ../001_structure/1O86_protein_nH_ncH.mol2
+ box_file                                  1O86.box.pdb
+ vdw_definition_file                       /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
+ score_grid_prefix                         grid
-Simplex Minimization Parameters
+If grid fails because it cannot find the .defn file, you may need to edit the path of the <code>vdw_definition_file</code> parameter to point to a VDW defn file that actually exists. It should be in the <code>parameters</code> folder of your DOCK6 installation.
-------------------------------------------------------------------------------------------
-                                              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
+Save the file and run using the following command:
-------------------------------------------------------------------------------------------
+  grid -i grid.in -o 1O86_gridinfo.out
-                                                   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
+An output file with your Grid generation will appear in your directory.
-------------------------------------------------------------------------------------------
-                                        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):
-------------------------------------------------------------------------------------------
+== 004: Minimization ==
-Could not open defn for reading.  Program will terminate.
+Before moving toward preforming docking of any fragments/ligands onto your receptor of interest it is important that your original ligand is energy-minimized. This is important before dock is able to calculate any energy interactions between atoms on the rector and ligand.
-(base) [ehspector@milan1 004_energymin]$ ls
+Move to your <code>~/tutorial/004_energy_min</code> directory and create an input file using:
-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
-  2019  2021  2023  2025            junk.txt     zzz.programs
-  2020  2022  2024  get_anchors.py  zzz.anchors
-(base) [ehspector@milan1 AMS536]$ cd zzz.programs/
-(base) [ehspector@milan1 zzz.programs]$ ls
-amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
-de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
-dock6.10         dock6.12         gen-frags-12         VS_libraries
-dock6.10_milan   dock6.12_ams536  old
-(base) [ehspector@milan1 zzz.programs]$ cd dock6.12_ams536/
-(base) [ehspector@milan1 dock6.12_ams536]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@milan1 dock6.12_ams536]$ cd parameters/
-(base) [ehspector@milan1 parameters]$ ls
-                         fraglib_linker.mol2         prot.table.ambcrg.sybH
-antechamber               fraglib_scaffold.mol2       sa_fraglib.dat
-chem.defn                 fraglib_sidechain.mol2      screen.in
-chemgrid                  fraglib_torenv.dat          screen.para
-chem_match.tbl            leap                        vdw_AMBER_parm94.defn
-flex.defn                 na.table.ambcrg             vdw_AMBER_parm94.dock3_7.defn
-flex_drive_mod.tbl        pains_table_2019_09_01.dat  vdw_AMBER_parm94.dock3_7_one_C_3.defn
-flex_drive.tbl            pains_table.dat             vdw_AMBER_parm96.defn
-flex_just_OH.defn         ph4.defn                    vdw_AMBER_parm99.defn
-flex_mod2.defn            prot.table.ambcrg.ambH      vdw_de_novo.defn
-flex_mod.defn             prot.table.ambcrg.pdb3H     vdw.parms.amb
-fraglib_ga_scaffold.mol2  prot.table.ambcrg.pdbH      vdw.parms.update.amb
-(base) [ehspector@milan1 parameters]$ pwd
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters
-(base) [ehspector@milan1 parameters]$ class
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/004_energymin/
-(base) [ehspector@milan1 004_energymin]$ vi min.in
-(base) [ehspector@milan1 004_energymin]$ touch max.in
-(base) [ehspector@milan1 004_energymin]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/
-(base) [ehspector@milan1 dock6.12_ams536]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@milan1 dock6.12_ams536]$ cd bin/
-(base) [ehspector@milan1 bin]$ ls
-am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
-amberize_complex   espgen        nchemgrid_GB          showbox
-amberize_ligand    grid          nchemgrid_SA          showsphere
-amberize_receptor  grid-convert  parmcal               solvgrid
-antechamber        grid-convrds  parmchk               solvmap
-atomtype           make_phimap   prepare_amber.pl      sphere_selector
-bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
-chemgrid           mol2.py       prepgen               teLeap
-combine_torenv.py  mopac         resp                  tleap
-dock6              mopac.sh      respgen
-(base) [ehspector@milan1 bin]$ pwd
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
-(base) [ehspector@milan1 bin]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/
-(base) [ehspector@milan1 5EEN]$ cd 004_energymin/
-(base) [ehspector@milan1 004_energymin]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i max.in
+ vi min.in
+In this input file, use the following parameters to minimize the ligand without re-orienting it:
---------------------------------------
+ conformer_search_type                                        rigid
-DOCK v6.12
+ use_internal_energy                                          yes
+ internal_energy_rep_exp                                      12
+ internal_energy_cutoff                                       100.0
+ ligand_atom_file                                             ../001_structure/1O86_ligand_wH_wcH.mol2
+ limit_max_ligands                                            no
+ skip_molecule                                                no
+ read_mol_solvation                                           no
+ calculate_rmsd                                               yes
+ use_rmsd_reference_mol                                       yes
+ rmsd_reference_filename                                      ../001_structure/1O86_ligand_wH_wcH.mol2
+ 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
+ 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
+ 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_drive.defn
+ flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
+ ligand_outfile_prefix                                        1O86_min
+ write_mol_solvation                                          no
+ write_orientations                                           no
+ num_scored_conformers                                        1
+ score_threshold                                              100.0
+ rank_ligands                                                 no
-Released September 2024
+Finally, run the minimization using DOCK6 as such:
-Copyright UCSF
+ dock6 -i min.in -o min.out
---------------------------------------
+The program should run relatively quickly and create a new Mol2 file called <code>1O86_min_ranked.mol2</code>. Download this file to your local machine and open it in Chimera along with the original <code>1O86_ligand_wH_wcH.mol2</code> to compare the pre- and post-minimized poses. There should be minimal difference between them.
-Conformational Sampling Parameters
+[[File:1O86_ligminoverlay.png|600px]]
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
-Internal Energy Parameters
+(note that in the above image hydrogens have been hidden for simplicity; the generated Mol2 file and the original ligand file should both be versions where hydrogens are present)
-------------------------------------------------------------------------------------------
-                                          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
+== 005: Rigid Docking ==
-------------------------------------------------------------------------------------------
+Rigid docking allows the ligand to be treated as a rigid molecule (no confirmational changes) and determines best orientation for molecule to fit directly into the receptor site.
-                                             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
+Move to your <code>~/tutorial/005_rigid_dock</code> directory and create an input file using the following command:
-------------------------------------------------------------------------------------------
+ vi rigid.in
-                                          use_database_filter [no] (yes no):
-Orient Ligand Parameters
+Add the following parameters:
-------------------------------------------------------------------------------------------
+ conformer_search_type                                        rigid
-                                                orient_ligand [yes] (yes no):no
+ use_internal_energy                                          yes
+ internal_energy_rep_exp                                      12
+ internal_energy_cutoff                                       100.0
+ ligand_atom_file                                             ../004_energy_min/1O86_min_scored.mol2
+ limit_max_ligands                                            no
+ skip_molecule                                                no
+ read_mol_solvation                                           no
+ calculate_rmsd                                               yes
+ use_rmsd_reference_mol                                       yes
+ rmsd_reference_filename                                      ../004_energy_min/1O86_min_scored.mol2
+ use_database_filter                                          no
+ orient_ligand                                                yes
+ automated_matching                                           yes
+ receptor_site_file                                           ../002_spheres/selected_spheres.sph
+ max_orientations                                             1000
+ critical_points                                              no
+ chemical_matching                                            no
+ use_ligand_spheres                                           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
+ 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
+ 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
+ ligand_outfile_prefix                                        1O86_rigid
+ write_mol_solvation                                          no
+ write_orientations                                           no
+ num_scored_conformers                                        100
+ write_conformations                                          no
+ cluster_conformations                                        yes
+ cluster_rmsd_threshold                                       2.0
+ score_threshold                                              100.0
+ rank_ligands                                                 no
-Bump Filter Parameters
+Run using the following command:
-------------------------------------------------------------------------------------------
+ dock6 -i rigid.in -o rigid.out
-                                                  bump_filter [no] (yes no):
-Master Score Parameters
+The job should take no longer than a minute.
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):
-Contact Score Parameters
+Or run using the following slurm script:
-------------------------------------------------------------------------------------------
+ #!/bin/bash
-                                        contact_score_primary [no] (yes no):
+ #SBATCH --job-name=1O86_rigid           # Name of the job
+ #SBATCH --output=rigid.txt  # Standard output file
+ #SBATCH --error=1O86_error.txt    # Standard error file
+ #SBATCH --ntasks-per-node=1        # Number of tasks (adjust as needed)
+ #SBATCH --mail-user=vanie.seecharan@stonybrook.edu          # user
+ #SBATCH --nodes=1                   # nodes
+ #SBATCH --time=4:00:00            # Maximum walltime (adjust as needed)
+ #SBATCH --partition=short-40core    # Correct partition name
+ # Ensure the input file exists before running the program
+ if [ ! -f grid.in ]; then
+    echo "Error: grid.in file not found!"
+    exit 1
+ fi
+ # Run the program
+ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i rigid.in -o rigid.out 10.0
-Grid Score Parameters
+The following output files will be produced in your directory:
-------------------------------------------------------------------------------------------
+* 1O86_rigid_scored.mol2
-                                           grid_score_primary [yes] (yes no):
+* rigid.out
-                                     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
+Download the Mol2 file to your computer. This Mol2 file will contain an ensemble of poses which will be messy to visualize all at once. As such, you should use Chimera's ViewDock functionality to view the rigid docked poses. Use Tools >> Surface/Binding Analysis >> ViewDock and open the <code>1O86_rigid_scored.mol2</code> file that was created in the docking. The file will be of type DOCK 4, 5, or 6. A separate dialogue box will open that will allow you to select which pose you would like to view.
-------------------------------------------------------------------------------------------
-MultiGrid Score Parameters
+[[File:1O86_rigiddockingviewdock2.png|600px]]
-------------------------------------------------------------------------------------------
-Dock3.5 Score Parameters
+== 006: Flexible Docking ==
-------------------------------------------------------------------------------------------
+Flexible docking accounts for the conformational flexibility of the ligand by sampling the torsions present in it.
-Continuous Energy Score Parameters
+Navigate to your <code>~/tutorial/006_flex_dock</code> and create an input file using the following command:
-------------------------------------------------------------------------------------------
+<pre>
+vi flex.in
+</pre>
-Footprint Similarity Score Parameters
+Add the following script:
-------------------------------------------------------------------------------------------
-Pharmacophore Similarity Score Parameters
+<pre>
-------------------------------------------------------------------------------------------
+conformer_search_type                                        flex
+write_fragment_libraries                                     no
-Hbond Energy Score Parameters
+user_specified_anchor                                        no
-------------------------------------------------------------------------------------------
+limit_max_anchors                                            no
+min_anchor_size                                              5
-Internal Energy Score Parameters
+pruning_use_clustering                                       yes
-------------------------------------------------------------------------------------------
+pruning_max_orients                                          1000
+pruning_clustering_cutoff                                    100
-Descriptor Score Parameters
+pruning_orient_score_cutoff                                  1000.0
-------------------------------------------------------------------------------------------
+pruning_conformer_score_cutoff                               100.0
+pruning_conformer_score_scaling_factor                       1.0
-Zou GB/SA Score Parameters
+use_clash_overlap                                            no
-------------------------------------------------------------------------------------------
+write_growth_tree                                            no
+use_internal_energy                                          yes
-Hawkins GB/SA Score Parameters
+internal_energy_rep_exp                                      12
-------------------------------------------------------------------------------------------
+internal_energy_cutoff                                       100.0
+ligand_atom_file                                             ../004_dock/1o86_lig_min_scored.mol2
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
-------------------------------------------------------------------------------------------
-                                              minimize_ligand [yes] (yes no):
-                                       simplex_max_iterations [1000] ():
-                               simplex_tors_premin_iterations [0] ():
-                                           simplex_max_cycles [1] ():
-                                       simplex_score_converge [0.1] ():
-                                       simplex_cycle_converge [1.0] ():
-                                           simplex_trans_step [1.0] ():
-                                             simplex_rot_step [0.1] ():
-                                            simplex_tors_step [10.0] ():
-                                            simplex_final_min [no] (yes no):
-                                          simplex_random_seed [0] ():
-                                        simplex_restraint_min [no] (yes no):yes
-                                simplex_coefficient_restraint [10.0] ():
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-                                                   atom_model [all] (all | united):
-                                                vdw_defn_file [vdw.defn] ():
-                                               flex_defn_file [flex.defn] ():
-                                              flex_drive_file [flex_drive.tbl] ():
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-                                        ligand_outfile_prefix [output] ():
-                                          write_mol_solvation [no] (yes no):
-                                           write_orientations [no] (yes no):
-                                        num_scored_conformers [1] ():
-                                              score_threshold [100.0] ():
-                                                 rank_ligands [no] (yes no):
-------------------------------------------------------------------------------------------
-Could not open vdw.defn for reading.  Program will terminate.
-(base) [ehspector@milan1 004_energymin]$ vimdiff min.in max.in
-files to edit
-(base) [ehspector@milan1 004_energymin]$ rm max.in
-(base) [ehspector@milan1 004_energymin]$ vi min.sh
-(base) [ehspector@milan1 004_energymin]$ vi min.in
-(base) [ehspector@milan1 004_energymin]$ bash min.sh
-(base) [ehspector@milan1 004_energymin]$ ls
-een.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan1 004_energymin]$ vi min.out
-(base) [ehspector@milan1 004_energymin]$ ls
-een.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan1 004_energymin]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ ls
-  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ mv 1086/ 1O86
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 1O86/commands.txt
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ ls
-commands.txt
-(base) [ehspector@milan2 1O86]$ bash commands.txt
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore
-  [Bookmarked Feb 7, 2025 at 3:22:42 PM]
-(base) [ehspector@milan2 1O86]$ mv 004_dock/ 004_energymin
-(base) [ehspector@milan2 1O86]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-(base) [ehspector@milan2 001_structure]$ ls
-O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
-O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-O86_surface.dms
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 5EEN]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-een.sph  5een_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/sphere.sph 1O86/002_surface_spheres/sphere.sph
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 1O86/002_surface_spheres/select.sph
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/INSPH 1O86/002_surface_spheres/INSPH
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-O86_surface.dms  INSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-At line 131 of file sphgen.f (unit = 4)
-Fortran runtime error: Cannot open file '5een_surface.dms': No such file or directory
-Error termination. Backtrace:
-#0  0x7ffff7d54ca5 in already_open
-	at ../../../libgfortran/io/open.c:742
-#1  0x404f73 in ???
-#2  0x40117c in ???
-#3  0x7ffff742958f in ???
-#4  0x7ffff742963f in ???
-#5  0x4011b4 in ???
-#6  0xffffffffffffffff in ???
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-At line 125 of file sphgen.f (unit = 6)
-Fortran runtime error: Cannot open file 'OUTSPH': File exists
-Error termination. Backtrace:
-#0  0x7ffff7d54ca5 in already_open
-	at ../../../libgfortran/io/open.c:742
-#1  0x404e9e in ???
-#2  0x40117c in ???
-#3  0x7ffff742958f in ???
-#4  0x7ffff742963f in ???
-#5  0x4011b4 in ???
-#6  0xffffffffffffffff in ???
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-At line 125 of file sphgen.f (unit = 6)
-Fortran runtime error: Cannot open file 'OUTSPH': File exists
-Error termination. Backtrace:
-#0  0x7ffff7d54ca5 in already_open
-	at ../../../libgfortran/io/open.c:742
-#1  0x404e9e in ???
-#2  0x40117c in ???
-#3  0x7ffff742958f in ???
-#4  0x7ffff742963f in ???
-#5  0x4011b4 in ???
-#6  0xffffffffffffffff in ???
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-At line 125 of file sphgen.f (unit = 6)
-Fortran runtime error: Cannot open file 'OUTSPH': File exists
-Error termination. Backtrace:
-#0  0x7ffff7d54ca5 in already_open
-	at ../../../libgfortran/io/open.c:742
-#1  0x404e9e in ???
-#2  0x40117c in ???
-#3  0x7ffff742958f in ???
-#4  0x7ffff742963f in ???
-#5  0x4011b4 in ???
-#6  0xffffffffffffffff in ???
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi 1086_new_surface.dms
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86_surface.dms  INSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86.sph  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86.sph  1O86_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 1O86]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
-O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
-(base) [ehspector@milan2 001_structure]$ ls
-O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
-O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ bash select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86_surface.dms  OUTSPH                select.sph
-O86.sph              INSPH             selected_spheres.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-_new_surface.dms  1O86_surface.dms  OUTSPH                select.sph
-O86.sph              INSPH             selected_spheres.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.sh 1O86/003_gridbox/showbox.sh
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.in 1O86/003_gridbox/showbox.in
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ bash showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-O86.box.pdb   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.sh 1O86/003_gridbox/grid.sh
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.in 1O86/003_gridbox/grid.in
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
-O86.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
-O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-O86.box.pdb   grid.in   grid.out   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.out
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-O86.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
- grid.bmp       grid.nrg   grid.sh   '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 1O86/004_energymin/min.sh
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 1O86/004_energymin/min.in
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/004_energymin/
-(base) [ehspector@milan2 004_energymin]$ vi min.in
-(base) [ehspector@milan2 004_energymin]$ cd ../001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-O86_ligand_H_cH.mol2      1O86_protein_H_cH.mol2
-O86_ligand_noH_nocH.mol2  1O86_protein_noH_nocH.mol2
-(base) [ehspector@milan2 001_structure]$ cd ../004_energymin/
-(base) [ehspector@milan2 004_energymin]$ ls
-min.in  min.sh
-(base) [ehspector@milan2 004_energymin]$ bash min.sh
-(base) [ehspector@milan2 004_energymin]$ ls
-O86.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan2 004_energymin]$ vi min.out
-(base) [ehspector@milan2 004_energymin]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 2w26]$ cd 001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-(base) [ehspector@milan2 001_structure]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_surface.dms  INSPH  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-At line 328 of file sphgen.f
-Fortran runtime error: Bad value during floating point read
-Error termination. Backtrace:
-#0  0x7ffff7d59e39 in formatted_transfer_scalar_read
-	at ../../../libgfortran/io/transfer.c:1790
-#1  0x7ffff7d5b535 in formatted_transfer
-	at ../../../libgfortran/io/transfer.c:2491
-#2  0x4049e0 in ???
-#3  0x40516a in ???
-#4  0x40117c in ???
-#5  0x7ffff742958f in ???
-#6  0x7ffff742963f in ???
-#7  0x4011b4 in ???
-#8  0xffffffffffffffff in ???
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_surface.dms
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_surface.dms  INSPH  OUTSPH  sphere.sph  temp1.ms  temp3.atc
-(base) [ehspector@milan2 002_surface_spheres]$ rm temp1.ms
-(base) [ehspector@milan2 002_surface_spheres]$ rm temp3.atc
-(base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26_surface.dms  INSPH  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
-(base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26.sph  2w26_surface.dms  INSPH  OUTSPH  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 2w26/002_surface_spheres/select.sph
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26.sph  2w26_surface.dms  INSPH  OUTSPH  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ../001_structure/
-(base) [ehspector@milan2 001_structure]$ ls
-w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
-w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
-(base) [ehspector@milan2 001_structure]$ cd ../002_surface_spheres/
-(base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ bash select.sph
-(base) [ehspector@milan2 002_surface_spheres]$ ls
-w26.sph  2w26_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
-(base) [ehspector@milan2 002_surface_spheres]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd 003_gridbox/
-(base) [ehspector@milan2 003_gridbox]$ ls
- grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ rm '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ ls
-grid.in  grid.sh  showbox.in  showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi showbox.in
-(base) [ehspector@milan2 003_gridbox]$ bash showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-w26.box.pdb   grid.in   grid.sh   showbox.in  '&showbox.log&'   showbox.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ vi grid.in
-(base) [ehspector@milan2 003_gridbox]$ vi grid.sh
-(base) [ehspector@milan2 003_gridbox]$ bash grid.sh
-(base) [ehspector@milan2 003_gridbox]$ ls
-w26.box.pdb   grid.in    grid.out   showbox.in       showbox.sh
- grid.bmp       grid.nrg   grid.sh   '&showbox.log&'
-(base) [ehspector@milan2 003_gridbox]$ vi grid.out
-(base) [ehspector@milan2 003_gridbox]$ cd ..
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox  005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_dock     006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 2w26]$ vi commands.txt
-(base) [ehspector@milan2 2w26]$ mv 004_dock/ 004_energymin
-(base) [ehspector@milan2 2w26]$ cd 004_energymin/
-(base) [ehspector@milan2 004_energymin]$ ls
-(base) [ehspector@milan2 004_energymin]$ ls
-(base) [ehspector@milan2 004_energymin]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 2w26/004_energymin/min.in
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/004_energymin/
-(base) [ehspector@milan2 004_energymin]$ vi min.in
-(base) [ehspector@milan2 004_energymin]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 2w26/004_energymin/min.sh
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan2 2w26]$ cd 004_energymin/
-(base) [ehspector@milan2 004_energymin]$ vi min.sh
-(base) [ehspector@milan2 004_energymin]$ bash min.sh
-(base) [ehspector@milan2 004_energymin]$ ls
-w26.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan2 004_energymin]$ vi min.out
-(base) [ehspector@milan2 004_energymin]$ client_loop: send disconnect: Broken pipe
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een.sph  5een_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan1 002_surface_spheres]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ home
-(base) [ehspector@milan1 espector]$ cd 4s0v/
-(base) [ehspector@milan1 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@milan1 4s0v]$ cd gas_teiger/
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas_2.in   gas_3.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
-gas_2.out  gas.in     no_charge            no_gas.out_scored.mol2
-gas_3.in   gas.out    no_gas.in            test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
-(base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@milan1 gas_teiger]$ ls
-gas_2.in   gas_3.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
-gas_2.out  gas.in     no_charge            no_gas.out_scored.mol2
-gas_3.in   gas.out    no_gas.in            test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas_2.out
-(base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
-(base) [ehspector@milan1 gas_teiger]$ vi test_mol2
-(base) [ehspector@milan1 gas_teiger]$ vi test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2
-(base) [ehspector@milan1 gas_teiger]$ cd ../../builds/alpha_branch/src/dock
-(base) [ehspector@milan1 dock]$ vi filter.cpp
-(base) [ehspector@milan1 dock]$ home
-(base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/
-(base) [ehspector@milan1 gas_teiger]$ pwd
-/gpfs/projects/rizzo/espector/4s0v/gas_teiger
-(base) [ehspector@milan1 gas_teiger]$ cp gas_2.in gas_4.in
-(base) [ehspector@milan1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_2.out  gas_4.in  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
-AAQ_yesG.mol2  gas_3.in   gas.in    no_charge            no_gas.out_scored.mol2
-gas_2.in        gas_3.out  gas.out   no_gas.in            test.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
-(base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
-(base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ vi gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/
-(base) [ehspector@milan1 5EEN]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
-(base) [ehspector@milan1 002_surface_spheres]$ ls
-een.sph  5een_surface.dms  INSPH  OUTSPH  selected_spheres.sph  select.sph  sphere.sph
-(base) [ehspector@milan1 002_surface_spheres]$ vi select.sph
-(base) [ehspector@milan1 002_surface_spheres]$ home
-(base) [ehspector@milan1 espector]$ cd ..
-(base) [ehspector@milan1 rizzo]$ home
-(base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/
-(base) [ehspector@milan1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_2.out  gas_4.in   gas.out              no_gas.in               test.mol2
-AAQ_yesG.mol2  gas_3.in   gas_4.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
-gas_2.in        gas_3.out  gas.in     no_charge            no_gas.out_scored.mol2
-(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ rm gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ vi gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_2.out  gas_4.in   gas.out              no_gas.in               test.mol2
-AAQ_yesG.mol2  gas_3.in   gas_4.out  gas.out_scored.mol2  no_gas.out              test_nocharge.mol2
-gas_2.in        gas_3.out  gas.in     no_charge            no_gas.out_scored.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
-(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_2.out  gas_4.in               gas.in               no_charge   no_gas.out_scored.mol2
-AAQ_yesG.mol2  gas_3.in   gas_4.out              gas.out              no_gas.in   test.mol2
-gas_2.in        gas_3.out  gas_4.out_scored.mol2  gas.out_scored.mol2  no_gas.out  test_nocharge.mol2
-(base) [ehspector@milan1 gas_teiger]$ vi gas_4.out_scored.mol2
-(base) [ehspector@milan1 gas_teiger]$ cp gas_4.in gas_5.in
-(base) [ehspector@milan1 gas_teiger]$ vi gas_5.in
-(base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_5.in -o gas_5.out
-(base) [ehspector@milan1 gas_teiger]$ vi gas_5.out
-(base) [ehspector@milan1 gas_teiger]$ home
-(base) [ehspector@milan1 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@milan1 dock]$ vi dockmol.cpp
-(base) [ehspector@milan1 dock]$ vi filter.cpp
-(base) [ehspector@milan1 dock]$ vi rdtyper.cpp
-(base) [ehspector@milan1 dock]$ vi dockmol.cpp
-(base) [ehspector@milan1 dock]$ cd ..
-(base) [ehspector@milan1 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@milan1 src]$ cd dock
-(base) [ehspector@milan1 dock]$ ls
-amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
-amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
-amber_typer.o       fingerprint.h         nab                   score_internal.o
-base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
-base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
-base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
-base_mpi.cpp        fraggraph.o           orient.h              score.o
-base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
-base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
-base_score.cpp      fragment.o            rddrive.h             score_ph4.o
-base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
-base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
-conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
-conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
-conf_gen_ag.o       grid.h                README                score_solvent.h
-conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
-conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
-conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
-conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
-conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
-conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
-conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
-conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
-conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
-conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
-conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
-conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
-conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
-conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
-conf_gen_hdb.o      lol                   score_footprint.h     trace.o
-defreal.h           Makefile              score_footprint.o     utils.cpp
-dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
-dockmol.cpp         master_conf.h         score_gist.h          utils.o
-dockmol.h           master_conf.o         score_gist.o          version.h
-dockmol.o           master_score.cpp      score.h               xlogp.cpp
-dock.o              master_score.h        score_hbond.cpp       xlogp.h
-filter.cpp          master_score.o        score_hbond.h
-filter.h            mem_info.cpp          score_hbond.o
-(base) [ehspector@milan1 dock]$ cd ..
-(base) [ehspector@milan1 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@milan1 src]$ cd ..
-(base) [ehspector@milan1 alpha_branch]$ ks
--bash: ks: command not found
-(base) [ehspector@milan1 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@milan1 alpha_branch]$ cd src/
-(base) [ehspector@milan1 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@milan1 src]$ cd ..
-(base) [ehspector@milan1 alpha_branch]$ cd install/
-(base) [ehspector@milan1 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@milan1 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 10 01:24:01 PM EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fingerprint.h:13,
-                 from fingerprint.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fingerprint.h:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fraggraph.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fraggraph.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fragment.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from gasteiger.h:8,
-                 from gasteiger.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from gasteiger.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from hungarian.h:7,
-                 from hungarian.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from hungarian.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from library_file.h:9,
-                 from library_file.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from library_file.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from limit_max_change.h:12,
-                 from limit_max_change.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from limit_max_change.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from master_conf.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from master_conf.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from master_score.cpp:2:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from master_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-^Cmake[1]: *** [../../install/rules.h:36: master_score.o] Interrupt
-make: *** [Makefile:28: dock] Interrupt
-(base) [ehspector@milan1 install]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Permission denied, please try again.
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 10 13:29:04 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-^Cmake[1]: *** [conf_gen_ag.o] Interrupt
-make: *** [dock] Interrupt
-(base) [ehspector@login2 install]$ rdkit
-bash: rdkit: command not found...
-(base) [ehspector@login2 install]$ rd
-srun: error: invalid partition specified: short-40core
-srun: error: Unable to allocate resources: Invalid partition name specified
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ rd
-srun: job 925032 queued and waiting for resources
-srun: job 925032 has been allocated resources
-(base) [ehspector@dn018 ~]$ home
-(base) [ehspector@dn018 espector]$ cd builds/alpha_branch/install/
-(base) [ehspector@dn018 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn018 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 10 13:31:12 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fingerprint.h:13,
-                 from fingerprint.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fingerprint.h:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fraggraph.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fraggraph.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fragment.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from gasteiger.h:8,
-                 from gasteiger.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from gasteiger.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from hungarian.h:7,
-                 from hungarian.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from hungarian.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from library_file.h:9,
-                 from library_file.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from library_file.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from limit_max_change.h:12,
-                 from limit_max_change.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from limit_max_change.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from master_conf.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from master_conf.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from master_score.cpp:2:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from master_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from orient.h:7,
-                 from orient.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from orient.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from sasa.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from sasa.h:14:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_amber.cpp:66:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_amber.cpp:55:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_chemgrid.cpp:39:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_chemgrid.cpp:38:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_descriptor.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_descriptor.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_footprint.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_footprint.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_ph4.h:7,
-                 from score_ph4.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_ph4.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_volume.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_volume.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_gist.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_gist.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_hbond.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_hbond.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_internal.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_internal.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_multigrid.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_multigrid.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_sasa.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_sasa.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_solvent.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_solvent.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from simplex.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from simplex.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from utils.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from utils.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.h:12,
-                 from iso_align.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fragment.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
-                 from rdtyper.cpp:18:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from rdtyper.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from rddrive.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from dockmol.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-cd nab && make all
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
-mv dock6.rdkit ../../bin
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Mon Feb 10 13:34:18 EST 2025.
-(base) [ehspector@dn018 install]$ exit
-exit
-(base) [ehspector@milan1 ~]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ home
-(base) [ehspector@milan1 espector]$ cd ..
-(base) [ehspector@milan1 rizzo]$ module load git
-(base) [ehspector@milan1 rizzo]$ home
-(base) [ehspector@milan1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan1 espector]$ git status
-fatal: not a git repository (or any parent up to mount point /)
-Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-(base) [ehspector@milan1 espector]$ cd builds/
-(base) [ehspector@milan1 builds]$ cd alpha_branch/
-(base) [ehspector@milan1 alpha_branch]$ git status
-On branch alpha_branch
-Your branch is up to date with 'origin/alpha_branch'.
-Changes not staged for commit:
-  (use "git add <file>..." to update what will be committed)
-  (use "git restore <file>..." to discard changes in working directory)
-	modified:   docs/new_in_6.13.txt
-	modified:   src/dock/filter.cpp
-Untracked files:
-  (use "git add <file>..." to include in what will be committed)
-	src/dock/lol
-	src/rdkit/boost/
-	src/rdkit/boost_1_71_0.tar.gz
-	src/rdkit/boost_1_71_0/
-	src/rdkit/eigen-3.3.9.tar.gz
-	src/rdkit/eigen-3.3.9/
-	src/rdkit/rdkit-Release_2019_09_1.tar.gz
-	src/rdkit/rdkit-Release_2019_09_1/
-no changes added to commit (use "git add" and/or "git commit -a")
-(base) [ehspector@milan1 alpha_branch]$ git commit src/dock/filter.cpp
-Aborting commit due to empty commit message.
-(base) [ehspector@milan1 alpha_branch]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 005_virtual_screen/
-(base) [ehspector@milan1 005_virtual_screen]$ ls
-(base) [ehspector@milan1 005_virtual_screen]$ cd ..
-(base) [ehspector@milan1 2w26]$ mv 005_virtual_screen/ 005_footprint/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_footprint           007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 005_footprint/
-(base) [ehspector@milan1 005_footprint]$ ls
-(base) [ehspector@milan1 005_footprint]$ touch footprint.in
-(base) [ehspector@milan1 005_footprint]$ ls
-footprint.in
-(base) [ehspector@milan1 005_footprint]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd 004_energymin/
-(base) [ehspector@milan1 004_energymin]$ ls
-w26.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan1 004_energymin]$ vi 2w26.lig.min_scored.mol2
-(base) [ehspector@milan1 004_energymin]$ ls
-w26.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan1 004_energymin]$ vi min.s
-(base) [ehspector@milan1 004_energymin]$ vi min.sh
-(base) [ehspector@milan1 004_energymin]$ cd ../
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_footprint           007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ vi commands.txt
-(base) [ehspector@milan1 2w26]$ cd ,,
--bash: cd: ,,: No such file or directory
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_footprint           007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 005_footprint/
-(base) [ehspector@milan1 005_footprint]$ ls
-footprint.in
-(base) [ehspector@milan1 005_footprint]$ mv footprint.in rigid.in
-(base) [ehspector@milan1 005_footprint]$ vi rigid.sh
-(base) [ehspector@milan1 005_footprint]$ cd ..
-(base) [ehspector@milan1 2w26]$ mv 005_footprint/ 005_rigid
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_rigid               007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 005_rigid/
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid.in  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ bash rigid.
-bash: rigid.: No such file or directory
-(base) [ehspector@milan1 005_rigid]$ bash rigid.sh
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
-Conformational Sampling Parameters
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-                                          use_internal_energy [yes] (yes no):
-                                      internal_energy_rep_exp [12] ():
-                                       internal_energy_cutoff [100.0] ():
-Note: Internal energy only includes repulsive VDW for growth and/or minimization.
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-                                             ligand_atom_file [database.mol2] ():
-                                            limit_max_ligands [no] (yes no):
-                                                skip_molecule [no] (yes no):
-                                           read_mol_solvation [no] (yes no):
-                                               calculate_rmsd [no] (yes no):
-Database Filter Parameters
-------------------------------------------------------------------------------------------
-                                          use_database_filter [no] (yes no):
-Orient Ligand Parameters
-------------------------------------------------------------------------------------------
-                                                orient_ligand [yes] (yes no):
-                                           automated_matching [yes] (yes no):
-                                           receptor_site_file [receptor.sph] ():
-                                             max_orientations [1000] ():
-                                              critical_points [no] (yes no):
-                                            chemical_matching [no] (yes no):
-                                           use_ligand_spheres [no] (yes no):
-Bump Filter Parameters
-------------------------------------------------------------------------------------------
-                                                  bump_filter [no] (yes no):
-Master Score Parameters
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):
-Contact Score Parameters
-------------------------------------------------------------------------------------------
-                                        contact_score_primary [no] (yes no):
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-                                           grid_score_primary [yes] (yes no):
-                                     grid_score_rep_rad_scale [1] ():
-                                         grid_score_vdw_scale [1] ():
-                                          grid_score_es_scale [1] ():
-                                          grid_lig_efficiency [no] (yes no):
-                                       grid_score_grid_prefix [grid] ():
-GIST Score Parameters
-------------------------------------------------------------------------------------------
-MultiGrid Score Parameters
-------------------------------------------------------------------------------------------
-Dock3.5 Score Parameters
-------------------------------------------------------------------------------------------
-Continuous Energy Score Parameters
-------------------------------------------------------------------------------------------
-Footprint Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Pharmacophore Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
-------------------------------------------------------------------------------------------
-                                              minimize_ligand [yes] (yes no):
-                                       simplex_max_iterations [1000] ():
-                               simplex_tors_premin_iterations [0] ():
-                                           simplex_max_cycles [1] ():
-                                       simplex_score_converge [0.1] ():
-                                       simplex_cycle_converge [1.0] ():
-                                           simplex_trans_step [1.0] ():
-                                             simplex_rot_step [0.1] ():
-                                            simplex_tors_step [10.0] ():
-                                            simplex_final_min [no] (yes no):
-                                          simplex_random_seed [0] ():
-                                        simplex_restraint_min [no] (yes no):
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-                                                   atom_model [all] (all | united):
-                                                vdw_defn_file [vdw.defn] ():
-                                               flex_defn_file [flex.defn] ():
-                                              flex_drive_file [flex_drive.tbl] ():
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-                                        ligand_outfile_prefix [output] ():
-                                          write_mol_solvation [no] (yes no):
-                                           write_orientations [no] (yes no):
-                                        num_scored_conformers [1] ():
-                                              score_threshold [100.0] ():
-                                                 rank_ligands [no] (yes no):
-------------------------------------------------------------------------------------------
-Could not open vdw.defn for reading.  Program will terminate.
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ rm rigid.in
-(base) [ehspector@milan1 005_rigid]$ touch rigid.in
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid.in  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ bash rigid.sh
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
-Conformational Sampling Parameters
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-                                          use_internal_energy [yes] (yes no):
-                                      internal_energy_rep_exp [12] ():
-                                       internal_energy_cutoff [100.0] ():
-Note: Internal energy only includes repulsive VDW for growth and/or minimization.
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-                                             ligand_atom_file [database.mol2] ():2w26.lig.min.mol2
-                                            limit_max_ligands [no] (yes no):
-                                                skip_molecule [no] (yes no):
-                                           read_mol_solvation [no] (yes no):
-                                               calculate_rmsd [no] (yes no):yes
-                                       use_rmsd_reference_mol [no] (yes no):yes
-                                      rmsd_reference_filename [ligand_rmsd.mol2] ():2w26.lig.min.mol2
-Database Filter Parameters
-------------------------------------------------------------------------------------------
-                                          use_database_filter [no] (yes no):
-Orient Ligand Parameters
-------------------------------------------------------------------------------------------
-                                                orient_ligand [yes] (yes no):
-                                           automated_matching [yes] (yes no):
-                                           receptor_site_file [receptor.sph] ():../002_surface_spheres/selected_spheres.sph
-                                             max_orientations [1000] ():
-                                              critical_points [no] (yes no):
-                                            chemical_matching [no] (yes no):
-                                           use_ligand_spheres [no] (yes no):
-Bump Filter Parameters
-------------------------------------------------------------------------------------------
-                                                  bump_filter [no] (yes no):
-Master Score Parameters
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):
-Contact Score Parameters
-------------------------------------------------------------------------------------------
-                                        contact_score_primary [no] (yes no):
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-                                           grid_score_primary [yes] (yes no):
-                                     grid_score_rep_rad_scale [1] ():
-                                         grid_score_vdw_scale [1] ():
-                                          grid_score_es_scale [1] ():
-                                          grid_lig_efficiency [no] (yes no):
-                                       grid_score_grid_prefix [grid] ():../003_gridbox/grid
-GIST Score Parameters
-------------------------------------------------------------------------------------------
-MultiGrid Score Parameters
-------------------------------------------------------------------------------------------
-Dock3.5 Score Parameters
-------------------------------------------------------------------------------------------
-Continuous Energy Score Parameters
-------------------------------------------------------------------------------------------
-Footprint Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Pharmacophore Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
-------------------------------------------------------------------------------------------
-                                              minimize_ligand [yes] (yes no):
-                                       simplex_max_iterations [1000] ():
-                               simplex_tors_premin_iterations [0] ():
-                                           simplex_max_cycles [1] ():
-                                       simplex_score_converge [0.1] ():
-                                       simplex_cycle_converge [1.0] ():
-                                           simplex_trans_step [1.0] ():
-                                             simplex_rot_step [0.1] ():
-                                            simplex_tors_step [10.0] ():
-                                            simplex_final_min [no] (yes no):
-                                          simplex_random_seed [0] ():
-                                        simplex_restraint_min [no] (yes no):
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-                                                   atom_model [all] (all | united):
-                                                vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_AMBER_parm99.defn
-                                               flex_defn_file [flex.defn] ():
-                                              flex_drive_file [flex_drive.tbl] ():
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-                                        ligand_outfile_prefix [output] ():rigid.out
-                                          write_mol_solvation [no] (yes no):
-                                           write_orientations [no] (yes no):
-                                        num_scored_conformers [1] ():
-                                              score_threshold [100.0] ():
-                                                 rank_ligands [no] (yes no):
-------------------------------------------------------------------------------------------
-Could not open flex.defn for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-Could not open flex_drive.tbl for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
-Initializing Library File Routines...
-Could not open 2w26.lig.min.mol2 for reading.  Program will terminate.
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ cp rigid.sh rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out
-(base) [ehspector@milan1 005_rigid]$ cd ../004_energymin/
-(base) [ehspector@milan1 004_energymin]$ ls
-w26.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan1 004_energymin]$ cd ../005_rigid/
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.out_scored.mol2  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.out_scored.mol2  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
-(base) [ehspector@milan1 005_rigid]$ cd ..
-(base) [ehspector@milan1 2w26]$ mv 006_virtual_screen_mpi/ 006_flex_docking
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_rigid         007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_flex_docking  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 005_rigid/
-(base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_rigid         007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_flex_docking  008_rescore        Notes.txt
-(base) [ehspector@milan1 2w26]$ cd 001_structure
-(base) [ehspector@milan1 001_structure]$ ls
-w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
-w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd 005_rigid/
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.out_scored.mol2  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
-(base) [ehspector@milan1 005_rigid]$ vi rigid.out
-(base) [ehspector@milan1 005_rigid]$ vi rigid.in
-(base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
-(base) [ehspector@milan1 005_rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.out_conformers.mol2  rigid.out_scored.mol2  rigid.sh
-(base) [ehspector@milan1 005_rigid]$ grep -c "Name" rigid.out_scored.mol2
-(base) [ehspector@milan1 005_rigid]$ client_loop: send disconnect: Broken pipe
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan1 ~]$ cd AMS_536/
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd ..
-(base) [ehspector@milan1 ~]$ cd ..
-(base) [ehspector@milan1 home]$ ls
-caaachase              dbobo               jksullivan     msazonova         skorada
-aaaggarwal            dcalabria           jktsui         mschedel          skotelnikov
-aaaggarwal.26FEB2020  dcazorla            jleehand       mschrimpf         skotla
-aabdurrob             dcbrown             jlfong         mschwaller        skrichevsky
-aabhilash             dcharan             jlguerra       mshaaban          skristam
-aadarsh               dchien              jlipshultz     mshahneousba      skrupp
-aadubois              ddassanis           jlomanto       mshih             sladerwager
-aagashe               ddelayo             jluceno        mshinder          slakshminara
-aagishtein            ddemartini          jlungu         mshu              slaverty
-aahern                ddukes              jlutsky        msilfies          slthomas
-aaiyer                deachen             jlweissman     msmoawad          smadishetty
-aajith                decarlson           jmaghakian     msrao             smaiti
-aakale                dekblom             jmarcantonio   msreeves          smallipattu
-aakiti                delam               jmarciano      mstanacevic       smamalis
-aakkumar              demccabe            jmayortorres   msweber           smartynenko
-aaksenova             dereliu             jmeliker       mtalukder         smascarenhas
-aaliang               deroy               jmendezmende   mthu              smconnors
-aallin                devlin              jmgentile      mtoledorozyc      smdick
-aallu                 dfarahmandpo        jmiao          mtsonev           smedved
-aalpern               dfei                jmitchell      mturk             smeghdadizan
-aamahmood             dfucich             jmorkos        mumarani          smelhiraj
-aambrown              dgaidhani           jmulackal      muprit            smesiha
-aamgalan              dgenet              jmurrugarral   mvalakonda        smhenry
-aaminev               dgersappe           jmurzaku       mvashishtha       smiduthuri
-aamurthy              dg-mgmt1-auth-keys  jmvasquez      mvfernandezs      smilakovic
-aanaggarwal           dg-mgmt2-auth-keys  jnassar        mvilensky         smirghafouri
-aanagnostopo          dgnatenko           jnatarajan     mwilking          smirroshande
-aanik                 dgoon               jnery          myarif            smofakham
-aaprasad              dgruzdev            jnicasio       myearsley         smui
-aarasappan            dgursoy             jnmauro        myoungblood       smukherjee
-aarefin               dgwood              jnong          mysql             smvaccaro
-aarmas                dhailegeorgi        joawilson      mzamani           snarmeen
-aarroyave             dhamam              jocai          mzepedaaguil      snigam
-aasim                 dhandzlik           jocwilliams    mzhang            snikhil
-aaslov                dhdesouza           jodey          naahassan         snimatullo
-aates                 dhildreth           jodoh          nabchowdhury      snizambad
-aaurora               dhongyi             jodweinstein   nabsyed           snolas
-aavadhani             dhperumal           joeleung       nacchen           snyman
-aavira                dhualong            joeychan       nacharya          soba
-aaydin                diannace            jofranklin     nagnihotri        sochakrabort
-aaysheth              disandovalch        johbernard     nagutierrez       sohshin
-ababbar               diwliu              johnliu        nalewis           sohtsuka
-abadhe                djagnarain          joifan         nanqwang          solhapark
-abahadori             djgold              jomyoung       napopova          somishra
-abaidya               djlambert           jonamartins    naqiu             somunoz
-aball                 djoh                jonicholson    nasweet           sooapark
-abardizbania          djulian             jonsu          natsai            sopjang
-abbhaskar             djyu                jonyin         nazzhou           sortizbetanc
-abeahmad              dkadams             joolee         nbalasubrama      sosarangi
-abenslama             dkharzeev           joosuh         nbasok            sosuresh
-abialkowska           dkirby              joroiland      nbayas            sowu
-abjoshi               dkozakov            joshmathew     nbodduluri        sozturk
-abkanevsky            dkunjadiya          joshumartin    nbosviel          spaci
-abogetti              dlanger             jovvazquezri   nbowers           spandrekar
-aborad                dlhe                joying         nciotoli          spang
-aborcatasciu          dlucksted           jozhao         ncmeloottu        spapazahario
-aborger               dmahalli            jpantano       ncpathak          spapazis
-aborowicz             dmahzabin           jparise        ndcertain         sparvathredd
-abozin                dmale               jparkinson     ndev              spathrose
-abphilip              dmarkov             jpascal        ndheilly          spilkey
-abrady                dmarr               jpcastillo     ndigrandi         spiret
-absalem               dmckinnon           jperezrios     ndnguyen          splee
-abtambe               dmirfenderes        jpeshansky     ndokania          spochron
-aburford              dmorenosanti        jpitt          ndurand           spothumahant
-acage                 dmukherjee          jpmoryl        ndzikowski        spriyadarsha
-acalder               dmulbagalven        jporavanthat   nesteves          spugach
-acali                 dnanjappa           jpwhite        nexposescan       sqavi
-acamino               dnimatullo          jqxiao         neyang            srahmani
-acastiblanco          dnterry             jranjan        nezheng           sraisinghani
-accapua               dobyrne             jrawski        nfaiza            sramanarajan
-acchakravart          dochoi              jrcheung       nfpugliese        sramanarajan.OLD
-acherath              dofu                jrcorbett      nganu             sramjan
-achouhan              dohhlee             jrest          nghoang           sramstrom
-acmarra               dokkang             jrgorman       ngitman           srashidian
-adamare               dongsong            jrimel         ngluck            sretineni
-adanial               dongwhan            jrkamler       ngujarati         srgupte
-adanoji               donshi              jrleeman       nhamdan           srnalluri
-adharan               dotan               jrojahn        nhirtle           srpayne
-adiloreto             doyjang             jrutledge      nichaturvedi      srshende
-ading                 dozhong             jrwei          nidimeglio        ssabaghian
-admannino             dpadhorny           jsaldivar      nigreen           ssagynbayeva
-adpeng                dpare               jsalley        nileong           ssandal
-adpollack             dparedesmeri        jsaltz         niranmanesh       ssarnot
-adrana                dparwana            jsaputo        nisankar          ssarwar
-adrflorio             dpati               jsaxena        nisong            sseepersaud
-adrogers              dpatil              jscanderson    nisoni            ssemerkant
-adubey                dpenchoff           jschuchart     nivsingh          sserbin
-adutt                 dpfennell           jschwedes      njschwartzap      sshaharia
-aecuomo               dpotemkin           jseeliger      nkahmed           sshapourmian
-aeichert              drendina            jseol          nkandru           ssheikhi
-aeltareb              drhamilton          jsgordon       nkatla            sshoque
-aeweiss               dschneble           jsinanan       nkdean            sshrestha
-afahmed               dseddoh             jsistla        nkeer             sshrivastava
-afarhadzadeh          dsforza             jskowalski     nkhalsa           ssivalenka
-afgregory             dshangase           jslogan        nkhandagale       ssjohn
-afrigo                dsingla             jsmaers        nkhatri           sskiena
-afurey                dsli                jsmucker       nkinalis          ssomani
-agaffoor              dslo                jsteier        nkinlock          ssperrottet
-agaikwad              dsmolarski          jsuchan        nkyose            sstoller
-agarforth             dstepanenko         jtalaveragre   nleak             sstoyanov
-agargueta             dstrenski           jtekverk       nlogozzo          ssundar
-agauer                dswesty             jtepan         nlrogers          ssunia
-aghai                 dthanassi           jtevans        nmahamud          ssyedfahad
-agilgomez             dtpham              jtgabrielli    nmaher            ssyritsyn
-agmaharaj             dtsybychev          jtjones        nmanzella         staralekar
-agnsinha              dtung               jtmessina      nmarcella         stawong
-agopalkrishn          duwwang             jtrelewicz     nmathew           stelehany
-agraikos              dvahabli            jtrue          nmehanna          sthaker
-agugel                dvyas               juaalcantara   nmeister          sthorgusen
-agulhane              dwhitty             juffeng        nmenasche         stjjiang
-ahalwah               dwiczer             julima         nmendiratta       stmandell
-ahc                   dwillcox            juliwu         nmeruva           stmccabe
-ahmkhan               dzavala             jumma          nmichielsen       stomar
-ahomayounnik          dziadlou            junding        nmitra            stpak
-ahsingh               eadas               jungshwang     nnadkarni         strainer
-ahurtado              earavera            junholee       nnaitlho          ststern
-ahxiao                eatkinson           junhuzhang     nnakka            stuznik
-aicheng               ebagherizade        junhyelee      nnawal            stzeng
-aidnani               ebartlett           junjiang       nnehaindrani      stzou
-ailyu                 eboria              junkang        nnghiemvu         sudkhan
-airussell             ebreen              junszhou       nniemiec          sukkumar
-ajacovelli            ebremer             juntyao        noibrahim         sunarasimhas
-ajalwan               ebrini              junwang5       nolconner         sunarasimhas.OLD
-ajamieson             ebryski             junxialiu      novsingh          sunghucho
-ajasniew              ecarcelespov        junywang       npahlavan         sunkim2
-ajchan                ecgross             jusandoval     npanagodawet      surmy
-ajchavez              echurch             juschan        nparghi           sushahid
-ajhong                eclemmon            jusliu         npasari           suwei
-ajkoller              ecline              jusong         npayen            svadnerkar
-ajlli                 ecoutsias           justili        npomata           svaldez
-ajmasella             ecowley             jusu           npregosin         svanderpoel
-ajoung                edeturk             juychen        nrajput           svayasi
-ajscarlatos           edma                juyyan         nramdin           svee
-ajtran                edowney             juzou          nreaton           swaxman
-ajwelsh               edzhang             jvansnellenb   nsalekfarama      swchaudhury
-ajyadav               eeryildiz           jvaska         nsampson          swen
-akalugade             efinson             jverbaarscho   nsehgal           sweverma
-akanodia              egebb               jvishal        nshouman          swpaul
-akapote               egentles            jvpepe         nsimakov          sxchen
-akarkare              egouvis             jvu            nsipperly         syaddanapudi
-akarzai               eheywood            jwahhab        nsmehta           syalla
-akaufman              ehspector           jwcross        nsoder            syarma
-akhibovska            ejcarey             jwcusick       nsokolow          syatigala
-akhosronejad          ejguan              jwisdom        nsomani           syatskar
-akhoukhi              ejli                jwlodek        nstreb            sydiaz
-akingan               ejohnfelt           jxue           ntadler           syousef
-akirillov             ekandov             jyerrick       ntardugno         sytlee
-akkale                ekbetancourt        jyluo          ntetrault         tabhatia
-akonosky              ekeck               jzoodsma       ntippabhatla      tadoyle
-akravchuk             ekeough             kabichandani   ntripti           taeklee
-akrowe                ekhew               kadeng         nvafaeinajaf      taeyounkim
-aktyagi               eklau               kadiallo       nvitek            tagiles
-akucich               ekoo                kadill         nvohra            tahkhan
-akuduregundi          elari               kadreher       nvsutherland      tajjung
-akundhuru             elettieri           kafarber       nwein             takther
-akverma               elgchan             kaifzheng      nwweber           talama
-akwakye               elharris            kaili          nxlee             talare
-alabella              eli                 kailiu2        nyfletcher        talin
-alaing                ellai               kailjiang      obellinson        tallison
-alanhuang             elleisenberg        kaimxu         odeshpande        tamislam
-alchung               elmlowe             kaitong        odiamond          tanis
-aldong                elogeswar           kaixichen      odickerson        taryu
-aldraper              elslattery          kamhassan      oeskiocak         tbabu
-alehsu                emacosta            kamrivera      ohaputhanthr      tbertino
-alem                  emarants            kanagarwal     ohyejin           tbrackins
-alexhernande          emarkowitz          kanzhao        okim              tbrinckmann
-alfwu                 emarzigliano        kapatel        okoren            tbrinkley
-algrullon             embriggs            kaporter       omcgranaghan      tburfeind
-alhhuang              emrlin              kapu           omorozova         tbushra
-alianwar              emroberts           karamachandr   omoy              tcanli
-alicwang              emyhand             kargill        onatu             tchatterton
-alietzau              enebet              kasong         oogunfolakan      tchristy
-alifeng               eoruro              katalwar       ooreilly          tchugh
-aliguori              eozkirimli          katschmidt     orambow           tcotroneo
-alindquist            epapadopoulo        kbaylous       osdeshpande       tdawar
-allekim               erandhawa           kbdiaz         oshakkour         tdiprima
-allelin               eraut               kbeckerredd    oshetty           tdviri
-allwong               erbraun             kbelfon        osteele           tema
-almabraham            erfan               kberard        oyang             testro
-almishra              erglukhov           kberghaus      oyasar            tgavryshko
-alokre                ericlin1            kccoughlin     padari            tglotch
-alowell               erizhou             kchetan        paggarwal         tgrgas
-alperezmendo          erkumar             kchitale       pahan             tgrossberndt
-alqin                 erluo               kdas           pallen            tguttula
-alsli                 erosenberg          kdavidson      pamishra          thamada
-alvhsu                errjones            kdehmelt       parjain           thausch
-alynegron             erschroeder         kdemir         parmitage         thdavidson
-amacinnis             erwhuang            kdevedzhiev    patflanagan       therault
-amaffei               esahin              kdhar          patmuller         therodrigues
-amanagarwal           esalman             kdhuri         pavkirkar         thollis
-amanpsingh            esaraivanov         kdyro          pavnkaur          thomlin
-amanzoor              eschiltzrous        kebui          pawu              thren
-amaresca              eshaji              keckartt       payao             thzhou
-amarya                eshetreatkle        kelam          pb                tianyuawang
-amassari              eshih               keliao         pbaliga           tili
-amasuno               eshuryak            kellywang      pcascantebon      timji
-ambbrown              esicoli             kelvlin        pcastillo         timshi
-amccumber             esiegmann           kenchin        pchinthamred      tinggao
-amcelroy              esogut              kenhu          pdalaya           tinghwu
-amchale               esonmez             kennwu         pdamore           tingliu2
-amcpherran            essingh             kereid         pdevarajan        tingslin
-amehla                eswong              kerwood        pdjuric           tinliu
-amehmood              etakeuchi           kevazquez      pdonat            tiwwong
-amgondal              etalis              kevcai         pdongle           tixi
-amibrahim             etchan              kevcheng       pdutta            tiyuan
-amigues               etcheung            keviliu        pechang           tjarrett
-amisaha               ethresher           kevwei         peihsieh          tjohannessen
-amkgupta              etmonaco            kexi           peinwang          tkarwal
-amnoonan              etrommer            kfatema        penzhang          tknoll
-amohamed              etsang              kfernando      pesun             tkohlmann
-amohammadrez          etwest              kflora         pferrero          tkral
-amohanty              etyen               kfryer         pgaikar           tkurc
-amohideen             evalin              kgarg          pganapathi        tla
-amoonilal             evaxie              kgayadhankar   pganesh           tlata
-amrabet               evergaracobo        kgcassar       pgodoy            tloden
-amramroop             evxie               kgjonas        pgoldbart         tlonsway
-amrangwala            ewpeterson          kgoranta       pgoriparthi       tmcgee
-amritpsingh           exiu                kgulati        pgubbala          tmia
-amullhaupt            eylei               khajny         pguo              tmohandas
-amychen5              eyzhu               khasegawa      pgurung           tmoriya
-amyla                 fabdinov            khoh           phariprasad       tmsmyth
-anadelgado            faliang             khumphries     phowlader         tmuntean
-analekseenko          falmodaresit        khyunjae       phtnguyen         tnle
-anarora               faluo               kihan          phyeh             tnsingletary
-ancollins             fang1               kim128         pinlee            toneal
-andcheung             fanliu2             kim169         pinliu            toye
-andguo                fannli              kim65          pjgriffin         tpalit
-andgutierrez          fanwang1            kingle         pkaelbling        tqduong
-andrchu               faoki               kipoon         pkayedpour        tqle
-andrwu                faslanbeigi         kisrani        pkidambi          traj
-andylin2              fatrahman           kissung        pkottapalli       trichen
-anearora              fatsai              kjamal         pkrstic           trli
-anegi                 faye                kjayanettiar   pkuan             trosenlicht
-aneiman               fayyang             kjroberts      pkwoczak          tsclement
-anejoshi              fbasharat           kjtorres       pliu              tshrestha
-anejoshi.OLD          fbischoff           kjun           plorenagodoy      tsinghal
-anemajerova           fcherat             kkamate        pmao              tslewis
-anfrenkel             fcornejofern        kkannapur      pmarla            tsmiley
-angderosa             fcoskun             kkasarapu      pmatera           tteng
-aniksingh             feliang             kkasavajhala   pmcdowall         tthakir
-anisrinivasa          fenzhang            kkaushik       pmdunge           tthulasidas
-anjmoore              fewang              kkayang        pmeade            ttnnguyen
-ankmaheshwar          feyeh               kkirane        pmeda             ttom
-ankrishnan            fgao                kkostyszyn     pmmehta           tweinacht
-anltran               fhchaudhry          kkui           pmscully          tweiwei
-annicoll              fiburke             kkurti         pmuzac            twymore
-anpnguyen             fiowong             kkyeong        pnalluri          txiang
-anpurwar              fjalia              klanzetta      pnookala          tye
-ansabharwal           fjangchup           klhudson       podonnell         tyeh
-ansgandhi             fkarankumar         kljjohnson     ppolak            tyokoyama
-anshen                fkhondker           kllivichuzca   ppriyadarshi      tzwei
-anslade               fladeind            kmadanahitib   praagarwal        uarora
-anthochen             fluo                kmardysilofa   pragupta          uarora.OLD
-antmunoz              fmaisha             kmasarik       praroy            ugarg
-antzhu                fmlopez             kmbala         pratagarwal       ukadakia
-anurizada             fmnoor              kmchang        pratkumar         umoll
-anvinod               fnieto              kmchau         priyjain          umukherjee
-anzaman               forabona            kmcneil        prkkumar          upoddar
-anzhu                 fpocaamoros         kmfallon       prmukhopadhy      urasheed
-anzzhou               frdominguezg        kmhayes        prouth            urehman
-aokisamen             frhu                kmsimon        prreddy           urosani
-apaddayurush          frobayobohor        kmueller       psahu             ushafiq
-apaddayurush.OLD      fsotiropoulo        kmungsoo       psamang           ushassan
-apagarwal             fuliang             kmurgas        psangtani         usunar
-apalit                fwelcome            kpallmann      psekar            utegshbayar
-apalo                 fzali               kpinzon        pshanbhogue       utumuluri
-apalve                gacolella           kpipitone      pskota            uuckun
-apamfilie             gahuja              kprose         psmeyer           uyevarouskay
-aperezantona          gakapoor            kralbano       psokol            vachandramou
-apettenati            gakhan              kramcharan     psonawane         vadabala
-aphope                galing              krayfield      psoundarapan      vanlin
-apilco                garrchen            krdonaldson    pssingh           vanugu
-apizzulli             gashna              krisharma      psurana           vassingh
-aplu                  gatran              krjain         psutter           vbabu
-apolanco              gaumoithe           krkehrli       ptitle            vbayevskiy
-apopoviciu            gazzhang            krmartin       ptonra            vbrill
-aporripiredd          gbalabhadra         krokosz        ptubiolo          vcacciola
-aprabhakar            gbalazsi            krtan          puzheng           vcarter
-apradeep              gbangera            ksabo          pvaishnavi        vchanana
-aprencis              gbermejo            ksampathkuma   pvaska            vduncan
-apsinghal             gbhattachary        kscardigno     pvemula           verana
-apytel                gbiselli            kschweitzer    pvespe            vgoel
-araghani              gbock               kshima         pximello          vhattibettam
-arahimyar             gbosilca            kshou          pyao              vhegde
-arahmati              gbrill              ksirapu        pzbarrett         vhnguyen
-aranasinghe           gchurchill          ksoumahoro     qiangwang         vhuynh
-aravula               gcma                kspuhler       qianywu           vicdai
-arbalasubram          gdhama              ksucich        qiaocwu           vidong
-arcurtis              gdjones             kswayze        qicao             viguo
-ardasgupta            gduarteramos        ktallman       qiding            vikamat
-ardowling             geliang             kthilanka      qihlin            villi
-areisel               gfiakos             ktsteven       qinie             vima
-aresnick              ggandem             ktuzinowski    qinjiang          vincewu
-arfali                ggeorgi             kuagarwal      qinren            vinmirandabr
-argiannakopo          ggopalkrishn        kuchan         qinzhao           vinzheng
-arglenn               gguleria            kumar1         qipan1            visheskumar
-arhossain             ghe                 kumar1.OLD     qirli             vissharma
-arjain                ghothi              kunli          qirwu             vivlam
-arjkrishna            gibrown             kuraj          qxiong            viyee
-armishra              gigill              kuzhong        raagarwal         vjana
-arobert               gimbriano           kveeramah      rabasu            vjishah
-arodriguezd           gipark              kvshah         rachatterjee      vkale
-arojain               girizzo             kwahlin        rachatterjee.OLD  vkhanikaeva
-arpahlavan            gito                kwwalton       rachowdhury       vkodumurumee
-arpbanerjee           gjfuentes           kwyu           raclam            vkondipati
-arpereira             gjiang              kwyyoo         radsrinivasa      vkootagaram
-arsaxena              gjkim               kyadav         raggarg           vlloyd
-arskhan               gkementzidis        kychao         ragte             vloganathan
-arumar                gkowzan             kyethiraj      rahhuang          vlokwani
-aryshrivasta          glarangeira         kylanglois     rahraja           vmaurya
-asadana               gmichaels           kymjames       raich             vmontanez
-asaji                 gmihalache          kyumin         raiislam          vpakala
-asakhan               gmiles              kzzhang        rairahman         vpamula
-asamala               gmogol              lahess         rajatkumar        vperkowski
-asamanta              gmoutsanidis        lawlin         rajdas            vranjan
-asamavedam            gmuradas            lbai           ramhuang          vratnala
-asatam                gnarh               lbozarth       ramorosso         vrustagi
-aschneble             gnwood              lcaradonna     rannadi           vseecharan
-aschorer              goconrosario        lchi           rapeaning         vsnu
-ashaalan              gparkar             lchrastecka    rashanbhag        vstaub
-asharfuddin           gperezgonzal        lcolleyndeso   rashizawa         vtangirala
-asheneman             gprachi             lcooke         ratwi             vvadia
-asillato              grahme              ldavalosalva   raychen2          vvedanair
-asingal               grapacciuolo        ldgraham       rbaheti           vvsharma
-askamat               grkulkarni          lecheung       rbasharat         wadawydiak
-askong                grperlman           ledong         rbertolini        waluo
-asmit                 gsantucci           ledwan         rbhal             wang110
-asofianopoul          gsbeglia            lee104         rbhansali         wang113
-asotocambres          gshivakumar         lee111         rbhowmik          wang132
-asoubki               gshu                lee75          rbiondo           wang148
-asparikh              gstokes             lehhou         rbird             wang154
-asrivastava           gsuczewski          leichen3       rbirnbaum         wang159
-asugumar              gtaylor             leili1         rbodenstein       wang54
-aszekely              guayang             leipan         rboseroy          wang84
-atannenbaum           guayu               leizhou        rbronstein        wangzhang
-ataouil               guazeng             leprentis      rburgert          wawen
-ateklu                guffeng             leriksson      rcconley          wayou
-ateplukhin            gurpreetsing        lernunez       rchabot           wazzhang
-athatikunta           guwechue            lessig         rckline           wbrett
-athennarasu           gvaillant           lesyan         rcrizzo           wcun
-athonis               gverma              letucker       rcsingh           wcunningham
-atosolini             gvorobyev           lgruenburg     rdavuluri         wdaniels
-atpradhan             gyoun               lhinners       rdefrancisco      wecui
-atripoli              gyzhang             lhthorne       rdhaipule         weibhuang
-atsegaimoore          gzakharov           li1            rdhawan           weicdeng
-atsenthilnat          gzborovsky          li20           rdhillon          weichang
-atvarghese            haawilliams         li3            rdogra            weichang.OLD
-aubutt                haenalee            li32           rdrocha           weicheng
-audupashanka          hagguo              liangzhu       rdrucker          weihong
-auhhuang              hahkhan             liannchen      rediaz            weihsu
-avaradarajan          haichwang           lichen8        refem             weihwang
-avisingh              hailxu              lichiang       relkin            weili3
-avonalbertin          hakcakaya           lifwang        relyu             weipeng
-avonderlinde          hallu               lihahuang      renunez           weishen
-avpatil               hamorales           lihazhang      rfkelly           weishi2
-avperry               hanhan              lihexu         rflood            weiszhong
-awalling              hanschoi            lihnguyen      rflorek           weitan
-awardah               hanxwu              lin56          rfrisina          weituchen
-awgriffith            hanzhou1            linchen3       rgadi             weizhu
-awills                haochuwang          lincyu         rgaonkar          welliao
-awjohnso              haolin1             lingjpan       rgautam           wenblu
-aydas                 haolyu              lingyang       rgiles            wenbwang
-ayedageresud          haorazhang          linjjiang      rgmillard         wendazhang
-ayedlarajaia          haotxu              linxu          rgonzalez         wendhu
-ayendluri             haowezheng          linyi          rgzhang           wendu
-ayepuri               haoyzheng           lirzheng       rhande            wendyang
-ayreddy               haraja              liszheng       rharrison         wenhgao
-aysaleem              harbhatt            liu36          rhelbock          wenjihuang
-ayshim                harlee              liu61          rherman           wensliu
-ayusrivastav          hasaadi             liuwang        rhesler           wentawu
-aziafat               hasmoon             liuyang2       rhoffren          wequ
-azuzow                hayyan              liuyzhou       rhua              whiwong
-babrahall             hazhan              liwyang        richatterjee      wholt
-bagarcia              hbchao              ljescobar      richkim           wihu
-ballam                hbien               lkarpuskasan   richlin           withomas
-baminazad             hborchert           lkassetti      rijayaraman       wiwang
-bangchen              hchawla             lko            rikaur            wixiang
-bastark               hchenwu             lkrug          rikeh             wjchen
-bavinash              hdle                llevack        riraquib          wknop
-bbelisle              hdonga              llingda        risjain           wlancer
-bboysan               hduong              lmadiraju      rispatil          wlian
-bbrendan              hechu               lmaeba         ritagarwal        wmichael
-bbulag                heekwon             lmanathungam   riwu              woaks
-bchauhan              henrwang            lmconnolly     rizhuang          wriggs
-bciranni              hetariq             lmdeoliveira   rjayaramared      wsander
-bclevine              hewwang             lmunad         rjbrowne          wsanderson
-bcolle                hhyao               lnazarov       rjdesmond         wshih
-bcuadrado             hipham              lnie           rjeyachandra      wsuttle
-bdanna                hjlynch             lnolasco       rjhuang           wthornton
-bdarapu               hjtrivedi           lonhan         rjleung           wweaver
-bdebarrosfer          hjudson             lorlowski      rjsoni            wweiqiao
-bdelamonica           hkaddour            loswanson      rjwillett         xbarron
-bding                 hkamran             lpanwang       rkhanal           xdmod
-beckert               hkhazaei            lparrillamon   rkhatwani         xiachu
-bejean                hkirby              lpbui          rkhot             xiamu
-bennliu               hle                 lpei           rkidambi          xianaliu
-benyu                 hleung              lpintodealme   rkoots            xiangyuhuang
-bessuman              hmainguy            lprowant       rkyatham          xiangyyang
-bewwong               hmdonaldson         lraguette      rlarsen           xiaocao
-bewwu                 hmoonam             lrastelli      rlpersaud         xiaodliu
-bezzheng              hmoura              lrole          rlsiford          xiaogli
-bfei                  hnegi               lsaleh         rmakheja          xiaohawang
-bfeole                hniederhause        lscampbell     rmalga            xiaohuliu
-bfochtman             hnnguyen            lschappell     rmandloi          xiaokzhao
-bfogg                 hoannguyen          lschutz        rmangalampal      xiaoleyang
-bfutcher              hogao               lshekhar       rmanku            xiaolhu
-bglevine              hokwak              lstrey         rmatsibekker      xiaolhuang
-bgoncalves            holiver             ltalbot        rmax              xiaolucheng
-bgourbal              honghuang           ltngo          rmenezes          xiaotiawang
-bgoyal                honglliu            ltorpey        rmoffitt          xiaotoli
-bguruvayoorm          honglu              ltorrehealy    rmohan            xiaoxyang
-bharrell              hongrzhu            luge           rmudhuganti       xiaoysun
-bhkumar               hongwchen           lujjia         rmuthu            xiaoyuli
-bhowlader             hongyuli            luoshi         rnarvekar         xiaoyuyang
-bhshin                honhuang            lusu           rnorthrup         xicao
-bhsiao                hotnguyen           luzou          rochandramoh      xichen10
-bighimire             hppatil             lvasanthakum   rodtan            xinachen
-bihyu                 hqaiser             lverma         roessig           xingma
-binnchen              hranjan             lvotapka       rohshukla         xingtzhou
-binzhou               hridout             lwollmuth      romjohnson        xingyichen
-bishi                 hrmohammed          lwreid         ronassar          xingywang
-bisshrestha           hrrajput            lyohe          ronwang           xingzguo
-bji                   hsarkar             lyrodrigues    root              xinhahuang
-bjkramer              hschang             maaibrahim     rorosenberg       xinlu2
-bjlai                 hsekino             maalynch       roshukla          xinqian
-bjlee                 hseyyedzadeh        maamandola     roychen1          xintang
-bjnelson              hshafiq             mabruzzeseot   rparsons          xinwang2
-bjqi                  hsiachang           madambrosio    rpatanwadia       xinwang5
-bjugan                hsingathala         madkar         rpatro            xinxu4
-bkhanikaev            hsirotkin           madowling      rpatwary          xinyazheng
-bkovarovic            hsnyders            maedelmann     rperna            xinyin
-blanunez              htalavera           maescobarrod   rpghosh           xiulzhang
-blukacsy              huang54             maggchen       rpmchugh          xiwhuang
-bluy                  huaxiao             maggonzalezg   rpohankar         xixxiong
-bmahal                huichen5            maghazahedi    rpopper           xizhang1
-bmariano              huideng             magmarkowska   rraghunathan      xji
-bmchapman             huidliu             maguevarra     rrani             xjiao
-bmhenn                huisong             mahahn         rristowhadli      xqliu
-bmhyland              huixu1              mahhasan       rritu             xsha
-bmkaufman             huixzhu             mahiralam      rsamulyak         xshuqian
-boakley               hullee              maiyedun       rsandhu           xuaqi
-bocao                 hungwchen           makhdhor       rsarker           xuaxu
-bohhuang              huntwale            makinboade     rsejour           xudeng
-boisuh                huyzhang            makmalone      rsher             xuebwang
-borwang               hvannieuwenh        makowalchyk    rshilkrot         xueqli
-bossun                hvig                maksen         rshimogawa        xuxie
-bowusufrimpo          hvijayakumar        maliyari       rsihag            xyuan
-bozhao1               hwoh                malvin         rsison            yaagarwal
-bpamuk                hxing               mamahzabin     rsmolinski        yakang
-bpilosov              hyejichoi           mamandola      rsoori            yang28
-bquang                hyemkim             mamlan         rspowers          yang34
-bquang.OLD            hyeocho             maochoa        rstusalitus       yangfwu
-brampanellid          hyeonkyung          mapak          rtamarkin         yangli10
-brbartlett            hykoo               mapang         rtelikicherl      yangli9
-brgraham              hymin               marif          rthacker          yanglu2
-brlai                 hyochung            marioreyes     rtrybulski        yangxie
-brlgonzalez           hyuchung            markhangelsk   ruhipatel         yangzhang
-brma                  hyulim              markong        ruicxu            yangzhou
-brmcgovern            hyunjuncho          masharma       ruiding           yanwang2
-brmoses               hyunsikim           masong         ruihechen         yaoli2
-brpark                hzhan               matique        ruiqiwang         yaozou
-brsantos              hzohair             matjones       ruishi            yashu
-brshao                iabbasparker        mattchang      rulliu            yaspatel
-brwwang               iakgun              mavanalstine   runcli            yaxuan
-bryang                iakim               mawwa          ruossun           yazadeh
-brzhou                ialabed             maxmuller      ruparekh          yazou
-brzhu                 ibilkhu             mazhao         rusharma          ybajaj
-bsbernstein           ibipul              mazzimontire   ruyu              ychao
-bschiller             ibolger             mbandham       rwales            yding
-bsen                  ibromberg           mbarbosa       rwilson           yehu
-bshan                 icisternino         mbastan        rxli              yejikim3
-bsheller              ifaridi             mbender        ryachen           yeke
-bsheridan             igkane              mbianchi       ryanglee          yellaham
-bspitzbart            igrehn              mbliss         ryao              yenwchen
-bsterling             ihubbard            mboisvert      rycchan           yenwechen
-bsundahl              iinani              mbolko         rychin            yeonskang
-btenreiro             ijacob              mborczuk       ryengel           yhannun
-btmichalowic          ijhuang             mbowen         rygeorge          yhasib
-buli                  ikao                mbozok         rysalernoeic      yhochberg
-bvilla                ikotler             mbrunger       rzlin             yibqi
-byungjkim             iloop               mbuskirk       saachowdhury      yichuang
-caaugustine           ilopezcoto          mcaponegro     saaikhan          yiclin
-caaventura            imarchitelli        mcfoley        sabedin           yicozhu
-calyu                 inikiforakis        mchio          sabergman         yidcheng
-camcdonough           iojima              mcirrito       sabeykoon         yifagao
-caponteriver          iosipitan           mckoch         sabousamra        yifasun
-caprea                iouthwaite          mclim          saconstantin      yifewu
-cargomes              iparaskevako        mcng           sadas             yigao2
-carhall               ipjohnson           mconners       sadeshpande       yihanwang
-carlliu               ipunn               mdabhole       sadsharma         yihsu
-carlopez              iramakrishna        mdarita        saerkim           yihua
-carty                 ishin               mdatar         saffan            yijiang3
-cballena              isiergiej           mdavariesfah   sagchandrash      yijing
-cbehan                istaylor            mdeisler       saichowdhury      yijliu
-cbetz                 itaradachuk         mdelasaysork   saihaque          yijtian
-cblackwell            itrivedi            mdhuang        saismail          yijzhu
-cboon                 iurbinahenri        mdovedytis     sakader           yiliu4
-cbrandon              ivalin              mdsweeney      sakhalifa         yilma
-cbudd                 ivanlin             mdwalam        sakinney          yimzhao
-cbunner               ivaratharaja        meemcnamara    sakotagiri        yimzhu
-ccardetti             iwankavala          meijli         samachen          yingczhou
-ccarew                jaapatel            meisanchezpe   samesingh         yingfan
-ccdressler            jabauer             meisong        samhoque          yinglu1
-ccgordon              jabryan             meliasi        samichowdhur      yinou
-cchecastaldo          jacacosta           meliot         samrosner         yinxzhang
-ccioffi               jaccao              memendi        samung            yinyou
-ccolosqui             jackili             mempark        samvasquez        yipli
-ccorbo                jacobsmith          menalam        sangyoon          yiqguo
-ccpeterson            jacojoseph          menchowdhury   sarani            yittian
-cdehury               jacparker           mengao         sasaluja          yiwasaki
-cdehury.OLD           jacsegal            mengjliu       sashrestha        yiwchao
-cdelorenzo            jaejeong            menglin1       sasnyder          yixcui
-cdreyer               jaevangelist        mengrzhang     sastephens        yiyayu
-cegarrison            jaeyojung           mengtliu       sasurana          yiyizhou
-celkhoury             jafinn              mengwu         saswang           yizholi
-cexu                  jafu                mengxwang      satsaha           yjetwani
-ceyeung               jagluzman           mesch          saukumar          ykakade
-cfeldman              jaharora            meserranosos   saupaul           ykhaliqui
-cflagg                jahua               meyasmin       saursingh         ykuyu
-cfnapoli              jaimehta            meyue          savargas          ymaung
-cfontanini            jakaczmarzyk        mezaman        saysharma         ymondal
-cforan                jakhil              mfbugallo      sazchowdhury      yneelam
-cgarybicas            jakkatz             mferdman       sbadlia           yohe
-cgauthier             jalbanes            mfierek        sbaines           yokato
-cgobler               jalbertigles        mfirmansyah    sbajjuri          yokee
-cgrieco               jalzamoramar        mfite          sbanam            yoki
-cgueli                jamarini            mforslund      sbatheja          yomma
-cguerraamori          jamoscosonun        mfoydl         sbeesabathun      yongjzhang
-chacho                jange               mfucci         sbeg              yongmchoi
-chahan                jannguyen           mgarciadiaz    sbenz             yongshin
-chalpern              janswong            mgcortes       sbhuma            yonxiang
-changhpark            jaschow             mghaderibane   sbillah           yoshen
-changjli              jashukla            mghogale       sbinnamangal      youcha
-chanzhang             jasjiang            mgholamianji   sbire             youngkwon
-charwong              jasolau             mgivehki       sbirrer           younkang
-chccai                jasonwang           mgwhite        sboddeti          yousshin
-chdang                jaswsingh           mhanubal       sboppudi          ypichkar
-chen110               jathoffman          mhare          sbrahmadevar      yrhamatzada
-chen147               jaygutierrez        mhaziz         sbscott           ysingh
-chen15                jazpurua            mhijikata      sburgert          ysoh
-chen157               jbak                mhorowitz      scberg            yson
-chen175               jbakalis            mhott          scduppala         ysoroka
-chen181               jbalsamo            miachristie    scentorrino       ytham
-chen182               jbarrantes          miahe          schheda           yuanjchen
-chen32                jbarron             mianchen       schiappone        yuanzhao
-chen77                jbernauer           mibbowman      schook            yuasong
-chencjiang            jbeutel             michaliang     scokro            yuchen4
-chenclu               jbhambure           michelhuang    scsteiger         yuchen7
-chenczhu              jbickel             michellhuang   sdedhia           yuchzhou
-chenghli              jbkelly             michhuang      sdefaz            yucma
-chengklin             jbohne              micnicolette   sdescalso         yucpu
-chengpsun             jbraick             micxu          sdhalleweyn       yucsun
-chenliang             jbrimlow            miczhao        sdisalvo          yucxing
-chetheringto          jbrunelle           miduan         sdivilov          yucye
-cheye                 jbuckley            mignatov       sdsouza           yudding
-chezheng              jbuckley.OLD        mihur          sdssingh          yudichen
-chgraham              jburzachiell        mijia          sebramirezvi      yuechen4
-chguo                 jcano               mijrivera      seg               yuefandeng
-chhhogan              jcaputi             milobi         seojchang         yuehuang
-chichiang             jcassella           miloska        seongan           yuejin
-chienlee              jcespedes           mimak          seonghjeong       yuewang6
-chihhchang            jchaillet           minghazhang    seongioh          yuewang7
-chihu                 jchivu              mingsun        seshin            yuewlin
-chiuyu                jchlee              mingyli        sestoller         yuezhao2
-chlow                 jcmichel            mingyzhang     seunchoi          yufchen
-chmorales             jcodere             minhwang       sexia             yuhajiang
-chodgdon              jcolaizzo           minkwan        sfardeen          yuhwu
-chou                  jcollier            miray          sfarhat           yulma
-chriskim              jconesa             mireza         sfarnan           yuluwang
-christwong            jdarling            miswong        sfinch            yulyu
-chtian                jdcraig             mjadhav        sfiola            yumichen
-chuahuang             jdeneau             mjavanmard     sfluo             yunhxu
-chugo                 jdesilva            mjbonney       sgajjala          yunjeon
-chuntchan             jdovi               mjchun         sgala             yunlzhang
-chuzhu                jdscully            mkaltak        sgenovese         yunpan
-chuzou                jdubnau             mkamiya        sghavamnia        yupeng
-chyou                 jdwarren            mkanasani      sghavat           yuqianwu
-chyyoon               jecao               mkanasani.OLD  sgholami          yuqiao
-chzuo                 jefzhong            mkapadia       sghorashi         yushuang
-cikang                jegaillard          mkaribian      sgopalan          yusjin
-ciriccio              jejchan             mkhemchandan   sgoswami          yuthe
-cjbyrnes              jelau               mkishore       sgrao             yuttian
-cjzheng               jelsoudy            mkochert       sgrieninger       yuwang7
-ckapre                jemak               mkoga          sgurram           yuwzhang
-ckarwan               jemchen             mkondeti       sguru             yuxia4
-ckelton               jenfu               mkonovalyuk    sgwilliams        yuxlin
-ckochath              jepace              mkoraiem       sgyuho            yuxuanzhang
-cksullivan            jerlin              mkpatel        shaamin           yuxushi
-cleeliang             jeryeung            mkritzer       shakislam         yuxwu
-clegett               jesgoldstein        mksanda        shalirou          yuyguo
-clfischer             jeslong             mkurakula      shanhe            yuzhwang
-clongarini            jessewang           mlaul          shanlin2          yyokoi
-clsears               jettran             mlauterbur     shaoliu           zafahmad
-cltong                jevalle             mlcollier      shaowang          zalseika
-cltucker              jeyeung             mlng           shaqin            zariahmed
-cluhmann              jeyyoo              mlondoo        sharinarayan      zballard
-clwolfe               jfmoon              mloverde       shawmathew        zbhinderwala
-cmack                 jgaige              mmadeira       shcchakrabor      zcheslog
-cmcarey               jgajello            mmahboob       shclay            zcytryn
-cmcgrew               jgergen             mmahim         shdesai           zdoora
-cmehndiratta          jglazar             mmaitra        shdixit           zdowling
-cmflynn               jglimm              mmakeev        shdixit.OLD       zdupont
-cmfoley               jgurevitch          mmarder        shechoi           zexizhang
-cmjurgensen           jhajagos            mmaskaliova    shengzhu          zeyao
-cmkennedy             jharder             mmasoumi       shengzwang        zezhu
-cmoczygemba           jheerwig            mmatero        shenjin           zfallon
-cmoote                jheinz              mmaung         sheshao           zgrandison
-cmorantesari          jheraghty           mmcduffie      shexiong          zgungor
-cmwoo                 jhjung              mmcneill       shikgupta         zhacai
-cnoe                  jhollister          mmerenstein    shilgupta         zhage
-cnoutsos              jhpark              mmilhaven      shilliu           zhagu
-codlam                jiabwang            mmimurphy      shiltian          zhang100
-cohwarner             jiachzhu            mmursheed      shitsai           zhang110
-cojiang               jiacxu              mniznikiewic   shivansharma      zhang118
-cokeoma               jiahuwang           mnovotny       shivgupta         zhang123
-coleary               jiajgao             moamin         shiyuawang        zhang133
-concao                jiaji               mobusan        shkhalid          zhang142
-conliu                jiakwang            moewilliams    shmmohammed       zhang152
-cpercival             jialai              moflus         shmondal          zhang173
-cpethe                jialin1             mogao          shopatel          zhanyang
-cpinizzotto           jiamili             mogoel         shperalta         zhaoliu
-cplizio               jiamwu              mohassan       shrajput          zhchai
-cprasad               jianfeng            mojia          shroy             zhddong
-cqiu                  jianflin            molssi000      shrraman          zhedzhang
-cradke                jianhan             molssi001      shsaha            zhefang
-crcollinswor          jianjliu            molssi002      shshekhar         zheng13
-crfernandesv          jianmtan            molssi003      shshekhar.OLD     zheng30
-csangiovanni          jiannyang           molssi004      shsin             zhengxwang
-csantoni              jianxiozhang        molssi005      shssridhar        zhenjhuang
-csasmith              jiaojiang           molssi006      shtao             zhenliu
-cschwaner             jiapatel            molssi007      shuaguo           zhenlu
-cshiveshwark          jiasu               molssi008      shubwang          zhenqian
-csiebor               jiatian             molssi009      shuhe             zhenwu
-csimmerling           jiawang1            molssi010      shujia            zhenxliu
-csingleton            jiaweichen          molssi011      shyyoo            zheychen
-cstussman             jiawezhu            molssi012      shyyuan           zhezhou1
-csyreilly             jiaxuyu             molssi013      shzzhou           zhibwang
-cthakur               jiayeguo            molssi014      siasun            zhibyang
-ctinker               jiayyan             molssi015      sichchen          zhideng
-ctustin               jibbai              molssi016      sicheliu          zhihhe
-cuwang                jichao              molssi017      sichhabra         zhihhuang
-cvorkas               jiddong             molssi018      sichliu           zhijli
-cweistuch             jiechen3            molssi019      sigadkar          zhimalin
-cwoellhof             jiemchen            molssi020      siggupta          zhipxu
-cxi                   jiemzeng            molssi021      sihqian           zhiwlin
-cyanagisawa           jienzhu             molssi022      sijhuang          zhixzhang
-cyluo                 jieyang             molssi023      sijjiang          zhiye
-cyoungflesh           jihlin              molssi024      sijliu            zhke
-czhen                 jihoopark           molssi025      silai             zhlee
-d9wang                jihuynh             molssi026      singanne          zhonliang
-dabelinsky            jihyepark           molssi027      singh4            zhouyu1
-dagolden              jiikim              molssi028      sinhong           zhuhli
-dagrange              jijin               molssi029      sinlin            zhuxie
-daiwang               jilao               molssi030      sinsmith          zhwong
-dalpancakmak          jiliu1              molssi031      sirle             zhxia
-damcintyre            jimlin              molssi032      sishizawa         zidiao
-damiruddin            jimun               molssi033      siskhakov         ziguan
-damoses               jin                 molssi034      siuchan           zijiao
-dandrew               jinghzhou           molssi035      siwewang          zijizhou
-dangelidis            jingwenli           molssi036      sixliu            zikhan
-danieliang            jingwezhang         molssi037      siyadav           zilinchen
-danitorresra          jingwliu            molssi038      siyao             zilwu
-danizheng             jinkokim            molssi039      siyimaya          zirliu
-dantorres             jinwang2            morahimi       siyzou            zishao
-dantyu                jinwei              moriasaranib   sizahid           ziweiwang
-danwei                jinyhu              mozhao         sizzheng          ziwyu
-daoconnell            jinyinwang          mperess        sjaffary          zixli
-dappark               jinyli              mpersch        sjamshad          ziyli
-darkow                jinyuyang           mpetrusky      sjeevan           ziyozhang
-darlin                jinyxu              mpkatz         sjens             ziyye
-darvind               jinzwang            mpsantomauro   sjiecheng         zkrayem
-darzeng               jiqian              mquispecarba   sjnelson          zlyu
-dathanasakos          jiychong            mradfar        sjyang            zmou
-daultmccoy            jiyim               mrahimibolda   skade             zniu
-davidlin              jiyjung             mrakhar        skagana           zoanderson
-davizhao              jiyounpark          mrashid        skalam            zoxie
-davliang              jiyuliu             mrathore       skalva            zqiao
-davsilverman          jiyuyang            mrayeesuddin   skann             zsongzhu
-dawan                 jjcarter            mrehan         skapse            zuzheng
-dawei                 jjguo               mreuter        skapur            zwray
-dawendt               jjjones             mrichter       skarnik           zye
-dawhu                 jjnielsen           mrius          skatariya         zzaidi
-daxxie                jkable              mrkumar        skavuri           zzhuang
-dayeung               jkiryluk            mrosati        sketchum          zzoya
-dayyan                jkodner             mrsun          skobayashi
-dayyoon               jkohara             msardis        skogilathota
-dbasu                 jkonopka            msavenkov      skomatireddy
-dbluestein            jkottmann           msayana        skoppuravuri
-(base) [ehspector@milan1 home]$ cd ..
-(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/
-(base) [ehspector@milan1 AMS536]$ ls
-EVE_Lig_nH.mol2    1eve_Rec_nH.mol2  2018  2021  2024            junk.txt
-EVE_Lig_wH.mol2    1eve_Rec_wH.mol2  2019  2022  2025            zzz.anchors
-EVE_Rec_nHDMS.dms  2017              2020  2023  get_anchors.py  zzz.programs
-(base) [ehspector@milan1 AMS536]$ cd 2025
-(base) [ehspector@milan1 2025]$ ls
-EVE_DOCK_VS      INSPH           rotations  wed_humpday.txt
-additional_files  robbashrc_file  test4.tar
-(base) [ehspector@milan1 2025]$ vi test4.tar
-(base) [ehspector@milan1 2025]$ pwd
-/gpfs/projects/AMS536/2025
-(base) [ehspector@milan1 2025]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/test4.tar test4.tar
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN  test4.tar
-(base) [ehspector@milan1 Tutorials]$ mv test4.tar 2w26/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin     007_cartesian_min  Notes.txt
-_surface_spheres  005_rigid         008_rescore        test4.tar
-_gridbox          006_flex_docking  commands.txt
-(base) [ehspector@milan1 2w26]$ tar -xf test4.tar
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin     007_cartesian_min  commands.txt
-_surface_spheres  005_rigid         008_rescore        Notes.txt
-_gridbox          006_flex_docking  2W26               test4.tar
-(base) [ehspector@milan1 2w26]$ cd 2W26/
-(base) [ehspector@milan1 2W26]$ ls
-_structure  002_spheres  003_grid  004_dock
-(base) [ehspector@milan1 2W26]$ cd 004_dock/
-(base) [ehspector@milan1 004_dock]$ ls
-fps_footprint_scored.txt      01fps_scored.mol2  02rgd.in           03fad.out
-fps_footprint_scored.txt.pdf  01fps.sh           02rgd.log          03fad_scored.mol2
-fps_hbond_scored.txt          01min.in           02rgd.out          03fad.sh
-fps.in                        01min.log          02rgd_scored.mol2  04flx.in
-fps.log1                      01min.out          02rgd.sh           04flx.sh
-fps.log2                      01min_scored.mol2  03fad.in           old_01min.in
-fps.out                       01min.sh           03fad.log
-(base) [ehspector@milan1 004_dock]$ vi 02rgd.in
-(base) [ehspector@milan1 004_dock]$ cd ../../
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin     007_cartesian_min  commands.txt
-_surface_spheres  005_rigid         008_rescore        Notes.txt
-_gridbox          006_flex_docking  2W26               test4.tar
-(base) [ehspector@milan1 2w26]$ mv 005_rigid/  005_dock/
-(base) [ehspector@milan1 2w26]$ mv 006_flex_docking/ 006_virtual_screening
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin          007_cartesian_min  commands.txt
-_surface_spheres  005_dock               008_rescore        Notes.txt
-_gridbox          006_virtual_screening  2W26               test4.tar
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_2w26
-(base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/02rgd.in 005_dock/
-(base) [ehspector@milan1 2w26]$ cd 005_dock/
-(base) [ehspector@milan1 005_dock]$ ls
-rgd.in    rigid.in   rigid.out_conformers.mol2  rigid.sh
-rigid_2.sh  rigid.out  rigid.out_scored.mol2
-(base) [ehspector@milan1 005_dock]$ rm rigid.in
-(base) [ehspector@milan1 005_dock]$ mv 02rgd.in rigid.in
-(base) [ehspector@milan1 005_dock]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.out_conformers.mol2  rigid.out_scored.mol2  rigid.sh
-(base) [ehspector@milan1 005_dock]$ rm rigid.out_conformers.mol2
-(base) [ehspector@milan1 005_dock]$ rm rigid.out_scored.mol2
-(base) [ehspector@milan1 005_dock]$ vi rigid.in
-(base) [ehspector@milan1 005_dock]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.sh
-(base) [ehspector@milan1 005_dock]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd 001_structure/
-(base) [ehspector@milan1 001_structure]$ la
--bash: la: command not found
-(base) [ehspector@milan1 001_structure]$ ls
-w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
-w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ../005_dock/
-(base) [ehspector@milan1 005_dock]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid.sh
-(base) [ehspector@milan1 005_dock]$ vi rigid.in
-(base) [ehspector@milan1 005_dock]$ mkdir rigid_docking
-(base) [ehspector@milan1 005_dock]$ mv rigid.in rigid_docking/
-(base) [ehspector@milan1 005_dock]$ mv rigid.sh rigid_docking/
-(base) [ehspector@milan1 005_dock]$ mv rigid_2.sh rigid_docking/
-(base) [ehspector@milan1 005_dock]$ rm rigid.out
-(base) [ehspector@milan1 005_dock]$ ls
-rigid_docking
-(base) [ehspector@milan1 005_dock]$ mkdir flex_docking
-(base) [ehspector@milan1 005_dock]$ mkdir_fixed_anchor_docking
--bash: mkdir_fixed_anchor_docking: command not found
-(base) [ehspector@milan1 005_dock]$ mkdir fixed_anchor_docking
-(base) [ehspector@milan1 005_dock]$ ls
-fixed_anchor_docking  flex_docking  rigid_docking
-(base) [ehspector@milan1 005_dock]$ cd rigid_docking/
-(base) [ehspector@milan1 rigid_docking]$ ls
-rigid_2.sh  rigid.in  rigid.sh
-(base) [ehspector@milan1 rigid_docking]$ vi rigid.in
-(base) [ehspector@milan1 rigid_docking]$ vi rigid_2.sh
-(base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
-(base) [ehspector@milan1 rigid_docking]$ ls
-rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
-(base) [ehspector@milan1 rigid_docking]$ vi rigid.out
-(base) [ehspector@milan1 rigid_docking]$ vi rigid.in
-(base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
-(base) [ehspector@milan1 rigid_docking]$ ls
-rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
-(base) [ehspector@milan1 rigid_docking]$ vi rigid.out
-(base) [ehspector@milan1 rigid_docking]$ vi rigid.in
-(base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
-(base) [ehspector@milan1 rigid_docking]$ ls
-rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
-(base) [ehspector@milan1 rigid_docking]$ grep -c "Name" rigid_scored.mol2
-(base) [ehspector@milan1 rigid_docking]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin          007_cartesian_min  Notes.txt
-_surface_spheres  005_dock               008_rescore        Robs_2w26
-_gridbox          006_virtual_screening  commands.txt       test4.tar
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/03fad.in 005_dock/fixed_anchor_docking/
-(base) [ehspector@milan1 2w26]$ cd 005_dock/fixed_anchor_docking/
-(base) [ehspector@milan1 fixed_anchor_docking]$ ls
-fad.in
-(base) [ehspector@milan1 fixed_anchor_docking]$ mv 03fad.in fad.in
-(base) [ehspector@milan1 fixed_anchor_docking]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cp rigid_docking/rigid_2.sh fixed_anchor_docking/fad.sh
-(base) [ehspector@milan1 005_dock]$ cd fixed_anchor_docking/
-(base) [ehspector@milan1 fixed_anchor_docking]$ ls
-fad.in  fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.in
-(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ bash fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ ls
-fad.in  fad.out  fad_scored.mol2  fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.out
-(base) [ehspector@milan1 fixed_anchor_docking]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cp fixed_anchor_docking/fad.sh flex_docking/flex.sh
-(base) [ehspector@milan1 005_dock]$ cd ..
-(base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/04flx.in 005_dock/flex_docking/flex.in
-(base) [ehspector@milan1 2w26]$ cd 005_dock/flex_docking/
-(base) [ehspector@milan1 flex_docking]$ ls
-flex.in  flex.sh
-(base) [ehspector@milan1 flex_docking]$ vi flex.in
-(base) [ehspector@milan1 flex_docking]$ vi flex.sh
-(base) [ehspector@milan1 flex_docking]$ bash flex.sh
-(base) [ehspector@milan1 flex_docking]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan1 flex_docking]$ grep -c "Name" flex_scored.mol2
-(base) [ehspector@milan1 flex_docking]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cd flex_docking/
-(base) [ehspector@milan1 flex_docking]$ pwd
-/gpfs/home/ehspector/AMS_536/Tutorials/2w26/005_dock/flex_docking
-(base) [ehspector@milan1 flex_docking]$ cd ../fixed_anchor_docking/
-(base) [ehspector@milan1 fixed_anchor_docking]$ ls
-fad.in  fad.out  fad_scored.mol2  fad.sh
-(base) [ehspector@milan1 fixed_anchor_docking]$ cd ../rigid_docking/
-(base) [ehspector@milan1 rigid_docking]$ ls
-rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
-(base) [ehspector@milan1 rigid_docking]$ cd ../../
-(base) [ehspector@milan1 2w26]$ cd ../
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/
-(base) [ehspector@milan1 5EEN]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan1 5EEN]$ mv 005_virtual_screen/ 005_dock
-(base) [ehspector@milan1 5EEN]$ cd 005_dock/
-(base) [ehspector@milan1 005_dock]$ ls
-(base) [ehspector@milan1 005_dock]$ mkdir rigid fixed_anchor flex
-(base) [ehspector@milan1 005_dock]$ ls
-fixed_anchor  flex  rigid
-(base) [ehspector@milan1 005_dock]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid_2.sh 5EEN/005_dock/rigid/
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/005_dock/rigid/
-(base) [ehspector@milan1 rigid]$ ls
-rigid_2.sh
-(base) [ehspector@milan1 rigid]$ vi rigid_2.sh
-(base) [ehspector@milan1 rigid]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 5EEN]$ cd 005_dock/
-(base) [ehspector@milan2 005_dock]$ ls
-fixed_anchor  flex  rigid
-(base) [ehspector@milan2 005_dock]$ cd rigid/
-(base) [ehspector@milan2 rigid]$ ls
-rigid_2.sh
-(base) [ehspector@milan2 rigid]$ touch rigid.in
-(base) [ehspector@milan2 rigid]$ vi rigid_2.sh
-(base) [ehspector@milan2 rigid]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i rigid.in
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
-Conformational Sampling Parameters
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-                                          use_internal_energy [yes] (yes no):
-                                      internal_energy_rep_exp [12] ():
-                                       internal_energy_cutoff [100.0] ():
-Note: Internal energy only includes repulsive VDW for growth and/or minimization.
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-                                             ligand_atom_file [database.mol2] ():5EEN.lig.min_scored.mol2
-                                            limit_max_ligands [no] (yes no):
-                                                skip_molecule [no] (yes no):
-                                           read_mol_solvation [no] (yes no):
-                                               calculate_rmsd [no] (yes no):yes
-                                       use_rmsd_reference_mol [no] (yes no):yes
-                                      rmsd_reference_filename [ligand_rmsd.mol2] ():5EEN.lig.min_scored.mol2
-Database Filter Parameters
-------------------------------------------------------------------------------------------
-                                          use_database_filter [no] (yes no):
-Orient Ligand Parameters
-------------------------------------------------------------------------------------------
-                                                orient_ligand [yes] (yes no):
-                                           automated_matching [yes] (yes no):
-                                           receptor_site_file [receptor.sph] ():../../002_surface_spheres/selected_spheres.sph
-                                             max_orientations [1000] ():
-                                              critical_points [no] (yes no):
-                                            chemical_matching [no] (yes no):
-                                           use_ligand_spheres [no] (yes no):
-Bump Filter Parameters
-------------------------------------------------------------------------------------------
-                                                  bump_filter [no] (yes no):
-Master Score Parameters
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):
-Contact Score Parameters
-------------------------------------------------------------------------------------------
-                                        contact_score_primary [no] (yes no):
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-                                           grid_score_primary [yes] (yes no):
-                                     grid_score_rep_rad_scale [1] ():
-                                         grid_score_vdw_scale [1] ():
-                                          grid_score_es_scale [1] ():
-                                          grid_lig_efficiency [no] (yes no):
-                                       grid_score_grid_prefix [grid] ():../../003_gridbox/grid
-GIST Score Parameters
-------------------------------------------------------------------------------------------
-MultiGrid Score Parameters
-------------------------------------------------------------------------------------------
-Dock3.5 Score Parameters
-------------------------------------------------------------------------------------------
-Continuous Energy Score Parameters
-------------------------------------------------------------------------------------------
-Footprint Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Pharmacophore Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
-------------------------------------------------------------------------------------------
-                                              minimize_ligand [yes] (yes no):yes
-                                       simplex_max_iterations [1000] ():
-                               simplex_tors_premin_iterations [0] ():
-                                           simplex_max_cycles [1] ():
-                                       simplex_score_converge [0.1] ():
-                                       simplex_cycle_converge [1.0] ():
-                                           simplex_trans_step [1.0] ():
-                                             simplex_rot_step [0.1] ():
-                                            simplex_tors_step [10.0] ():
-                                            simplex_final_min [no] (yes no):
-                                          simplex_random_seed [0] ():
-                                        simplex_restraint_min [no] (yes no):
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-                                                   atom_model [all] (all | united):
-                                                vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
-                                               flex_defn_file [flex.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-                                              flex_drive_file [flex_drive.tbl] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-                                        ligand_outfile_prefix [output] ():rigid
-                                          write_mol_solvation [no] (yes no):
-                                           write_orientations [no] (yes no):
-                                        num_scored_conformers [1] ():
-                                              score_threshold [100.0] ():
-                                                 rank_ligands [no] (yes no):
-------------------------------------------------------------------------------------------
-Initializing Library File Routines...
-Could not open 5EEN.lig.min_scored.mol2 for reading.  Program will terminate.
-(base) [ehspector@milan2 rigid]$ cd ../../004_energymin/
-(base) [ehspector@milan2 004_energymin]$ ls
-een.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan2 004_energymin]$ cd ../005_dock/rigid/
-(base) [ehspector@milan2 rigid]$ ls
-rigid_2.sh  rigid.in
-(base) [ehspector@milan2 rigid]$ vi rigid.in
-(base) [ehspector@milan2 rigid]$ vi rigid.in
-(base) [ehspector@milan2 rigid]$ bash rigid_2.sh
-(base) [ehspector@milan2 rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out
-(base) [ehspector@milan2 rigid]$ vi rigid.out
-(base) [ehspector@milan2 rigid]$ vi rigid.in
-(base) [ehspector@milan2 rigid]$ bash rigid_2.sh
-(base) [ehspector@milan2 rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid_scored.mol2
-(base) [ehspector@milan2 rigid]$ vi rigid.out
-(base) [ehspector@milan2 rigid]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/
-(base) [ehspector@milan2 rigid]$ rm rigid.in
-(base) [ehspector@milan2 rigid]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid.in 5EEN/005_dock/rigid/rigid.in
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/
-(base) [ehspector@milan2 rigid]$ ls
-rigid_2.sh  rigid.in  rigid.out  rigid_scored.mol2
-(base) [ehspector@milan2 rigid]$ vi rigid.in
-(base) [ehspector@milan2 rigid]$ bash rigid_2.sh
-(base) [ehspector@milan2 rigid]$ ls
-rigid_2.sh  rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2
-(base) [ehspector@milan2 rigid]$ grep -c "Name" rigid_scored.mol2
-(base) [ehspector@milan2 rigid]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.in 5EEN/005_dock/fixed_anchor/fad.in
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.sh 5EEN/005_dock/fixed_anchor/fad.sh
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/fixed_anchor/
-(base) [ehspector@milan2 fixed_anchor]$ ls
-fad.in  fad.sh
-(base) [ehspector@milan2 fixed_anchor]$ vi fad.in
-(base) [ehspector@milan2 fixed_anchor]$ vi fad.sh
-(base) [ehspector@milan2 fixed_anchor]$ bash fad.sh
-(base) [ehspector@milan2 fixed_anchor]$ ls
-fad.in  fad.out  fad_scored.mol2  fad.sh
-(base) [ehspector@milan2 fixed_anchor]$ grep -c "Name" fad_scored.mol2
-(base) [ehspector@milan2 fixed_anchor]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.in 5EEN/005_dock/flex/flex.in
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.sh 5EEN/005_dock/flex/flex.sh
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
-(base) [ehspector@milan2 flex]$ ls
-flex.in  flex.sh
-(base) [ehspector@milan2 flex]$ vi flex.in
-(base) [ehspector@milan2 flex]$ bash flex.sh
-exit
-(base) [ehspector@milan2 flex]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2
-(base) [ehspector@milan2 flex]$ vi flex.out
-(base) [ehspector@milan2 flex]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ rm flex.out
-(base) [ehspector@milan2 flex]$ bash flex.sh
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ vi flex.
-(base) [ehspector@milan2 flex]$ vi flex.out
-(base) [ehspector@milan2 flex]$ cd ..
-(base) [ehspector@milan2 005_dock]$ ls
-fixed_anchor  flex  rigid
-(base) [ehspector@milan2 005_dock]$ cd flex/
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_virtual_screen      007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 1O86]$ mv 005_virtual_screen/ 005_dock
-(base) [ehspector@milan2 1O86]$ cd 005_dock/
-(base) [ehspector@milan2 005_dock]$ mkdir rigid fixed_anchor flex
-(base) [ehspector@milan2 005_dock]$ cd ../../
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.in 1O86/005_dock/rigid/rigin.in
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.sh 1O86/005_dock/rigid/rigin.sh
-cp: cannot stat '5EEN/005_dock/rigid/rigid.sh': No such file or directory
-(base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid_2.sh 1O86/005_dock/rigid/rigin.sh
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/005_dock/rigid/
-(base) [ehspector@milan2 rigid]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP AMS_548 % cd ../AMS_691
-(base) supremestudier@Evans-MBP AMS_691 % ls
-AMS691_01.pdf	Lectures	Projects	Text_book
-(base) supremestudier@Evans-MBP AMS_691 % mkdir PyTorch
-(base) supremestudier@Evans-MBP AMS_691 % cd ../AMS_536
-(base) supremestudier@Evans-MBP AMS_536 % ls
-Tutorial				project.example.dGhyd.pdf
-project.example.MMPS.pdf		zzz_2025_01_29a_seawulf_notes.docx
-(base) supremestudier@Evans-MBP AMS_536 % cd Tutorial
-(base) supremestudier@Evans-MBP Tutorial % ls
-O86		2w26		5EEN		folders.txt
-(base) supremestudier@Evans-MBP Tutorial % cd 5EEN
-(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ cd 1O86/005_dock/rigid/
--bash: cd: 1O86/005_dock/rigid/: No such file or directory
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd 1O86/005_dock/rigid/
--bash: cd: 1O86/005_dock/rigid/: No such file or directory
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/rigid/
-(base) [ehspector@milan1 rigid]$ ls
-rigin.in  rigin.sh
-(base) [ehspector@milan1 rigid]$ mv rigin.in rigid.in
-(base) [ehspector@milan1 rigid]$ mv rigin.sh rigid.sh
-(base) [ehspector@milan1 rigid]$ vi rigid.in
-(base) [ehspector@milan1 rigid]$ cd ../../004_energymin/
-(base) [ehspector@milan1 004_energymin]$ ls
-O86.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan1 004_energymin]$ cd ../005_dock/rigid/
-(base) [ehspector@milan1 rigid]$ ls
-rigid.in  rigid.sh
-(base) [ehspector@milan1 rigid]$ vi rigid.sh
-(base) [ehspector@milan1 rigid]$ bash rigid.sh
-(base) [ehspector@milan1 rigid]$ ls
-rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
-(base) [ehspector@milan1 rigid]$ vi rigid.out
-(base) [ehspector@milan1 rigid]$ grep -c "Name" rigid_scored.mol2
-(base) [ehspector@milan1 rigid]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cd ../../
-(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.in 1O86/005_dock/fixed_anchor/fad.in
-(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.sh 1O86/005_dock/fixed_anchor/fad.sh
-(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.in 1O86/005_dock/flex/flex.in
-(base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.sh 1O86/005_dock/flex/flex.sh
-(base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/fixed_anchor/
-(base) [ehspector@milan1 fixed_anchor]$ ls
-fad.in  fad.sh
-(base) [ehspector@milan1 fixed_anchor]$ vi fad.in
-(base) [ehspector@milan1 fixed_anchor]$ bash fad.sh
-(base) [ehspector@milan1 fixed_anchor]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cd fixed_anchor/
-(base) [ehspector@milan1 fixed_anchor]$ ls
-fad.in  fad.out  fad_scored.mol2  fad.sh
-(base) [ehspector@milan1 fixed_anchor]$ grep -c "Name" fad_scored.mol2
-(base) [ehspector@milan1 fixed_anchor]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cd flex/
-(base) [ehspector@milan1 flex]$ ls
-flex.in  flex.sh
-(base) [ehspector@milan1 flex]$ vi flex.in
-(base) [ehspector@milan1 flex]$ bash flex.sh
-^C^X
-(base) [ehspector@milan1 flex]$ vi flex.in
-(base) [ehspector@milan1 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan1 flex]$ rm flex.out
-(base) [ehspector@milan1 flex]$ bash flex.sh
-(base) [ehspector@milan1 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan1 flex]$ vi flex.out
-(base) [ehspector@milan1 flex]$ grep -c "Name" flex_scored.mol2
-(base) [ehspector@milan1 flex]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/005_dock/flex_docking/
-(base) [ehspector@milan1 flex_docking]$ vi flex.in
-(base) [ehspector@milan1 flex_docking]$ cd ..
-(base) [ehspector@milan1 005_dock]$ cd ../../5EEN/005_dock/flex/
-(base) [ehspector@milan1 flex]$ vi flex.in
-(base) [ehspector@milan1 flex]$ exit
-(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-****IMPORTANT MESSAGE BELOW****
-In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/
-(base) [ehspector@login2 install]$ ls
-bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
-bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
-config.h   gnu.parallel        ibmaix                   Makefile        test
-configure  gnu.parallel.rdkit  intel                    oneapi
-docker     gnu.rdkit           intel.intelmpi.parallel  pgi
-gnu        gnu.valgrind        intel.ip.mkl             rules.h
-(base) [ehspector@login2 install]$ ./configure gnu
-The requested configuration file was found.
-Warning: the configuration file already exists with the creation stamp:
-# Created at Mon Jan 20 04:34:02 PM EST 2025 via ./configure gnu.rdkit
-It will be overwritten !
-Don't forget to make clean before rebuilding.
-To reconfigure and rebuild everything start with make -i distclean:
-Reconfiguring after make -i distclean will avoid this warning.
-The DOCK configuration file has been created.
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Wed Feb 12 10:29:40 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
-g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
-g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
-g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
-g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
-g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
-g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
-g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
-g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
-g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
-g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
-g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
-g++ -c -O2 -std=c++11 -o score.o  score.cpp
-g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
-g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
-g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
-g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
-g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
-g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
-g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
-g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
-g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
-g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
-g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
-g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
-g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
-g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
-g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
-g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
-g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
-cd nab && make all
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-lm -lpthread
-mv dock6 ../../bin
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Wed Feb 12 10:31:34 EST 2025.
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ..
-(base) [ehspector@login2 src]$ cd ../install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Wed Feb 12 10:33:23 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:550:9: error: ‘num_zeros’ was not declared in this scope
-|     if (num_zeros == mol.num_atoms){
-      |         ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-make[1]: *** [dockmol.o] Error 1
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [dock] Error 2
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ../
-(base) [ehspector@login2 src]$ cd ../install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Wed Feb 12 10:36:16 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
-g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
-g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
-g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
-g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
-g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
-g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
-g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
-g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
-g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
-g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
-g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
-g++ -c -O2 -std=c++11 -o score.o  score.cpp
-g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
-g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
-g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
-g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
-g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
-g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
-g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
-g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
-g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
-g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
-g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
-g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
-g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
-g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
-g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
-g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
-g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
-cd nab && make all
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-lm -lpthread
-mv dock6 ../../bin
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Wed Feb 12 10:38:00 EST 2025.
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd ,,
--bash: cd: ,,: No such file or directory
-(base) [ehspector@login2 alpha_branch]$ home
-(base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2   gas_4.in               gas.in               no_gas.out_scored.mol2
-AAQ_yesG.mol2  gas_4.out              gas.out              test.mol2
-gas_2.in        gas_4.out_scored.mol2  gas.out_scored.mol2  test_nocharge.mol2
-gas_2.out       gas_5.in               no_charge
-gas_3.in        gas_5.out              no_gas.in
-gas_3.out       gas_5.out_scored.mol2  no_gas.out
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.out
-(base) [ehspector@login2 gas_teiger]$ rm gas_4.out
-(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas.out
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2   gas_3.out              gas_5.out_scored.mol2  no_gas.in
-AAQ_yesG.mol2  gas_4.in               gas.in                 no_gas.out
-gas_2.in        gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-gas_2.out       gas_5.in               gas.out_scored.mol2    test.mol2
-gas_3.in        gas_5.out              no_charge              test_nocharge.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.out
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login2 gas_teiger]$ vi gas_5.in
-(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2
-(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2
-(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_5.in -o gas_5.out
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2   gas_3.out              gas_5.out_scored.mol2  no_gas.in
-AAQ_yesG.mol2  gas_4.in               gas.in                 no_gas.out
-gas_2.in        gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-gas_2.out       gas_5.in               gas.out_scored.mol2    test.mol2
-gas_3.in        gas_5.out              no_charge              test_nocharge.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_5.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_5.in
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2   gas_4.in               gas.in               no_gas.out_scored.mol2
-AAQ_yesG.mol2  gas_4.out              gas.out              test.mol2
-gas_2.in        gas_4.out_scored.mol2  gas.out_scored.mol2  test_nocharge.mol2
-gas_2.out       gas_5.in               no_charge
-gas_3.in        gas_5.out              no_gas.in
-gas_3.out       gas_5.out_scored.mol2  no_gas.out
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.out
-(base) [ehspector@login2 gas_teiger]$ cd ..
-(base) [ehspector@login2 4s0v]$ cd ..
-(base) [ehspector@login2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@login2 dock]$ vi filter.cpp
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ..
-(base) [ehspector@login2 src]$ cd ../install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Wed Feb 12 10:49:54 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:542:5: error: ‘If’ was not declared in this scope
-|     If all partial charges are zero, it is a bad molecule
-      |     ^~
-dockmol.cpp:546:13: error: ‘num_zeros’ was not declared in this scope
-|             num_zeros += 1;
-      |             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp:549:6: error: ‘Is’ was not declared in this scope
-|      Is it a bad molecule?
-      |      ^~
-dockmol.cpp:552:7: error: ‘else’ without a previous ‘if’
-|     } else {
-      |       ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-make[1]: *** [dockmol.o] Error 1
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [dock] Error 2
-(base) [ehspector@login2 install]$ cd ../src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ..
-(base) [ehspector@login2 src]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd src/dock
-(base) [ehspector@login2 dock]$ cd ../../
-(base) [ehspector@login2 alpha_branch]$ cd install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Wed Feb 12 10:52:33 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
-g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
-g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
-g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
-g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
-g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
-g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
-g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
-g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
-g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
-g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
-g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
-g++ -c -O2 -std=c++11 -o score.o  score.cpp
-g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
-g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
-g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
-g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
-g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
-g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
-g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
-g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
-g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
-g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
-g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
-g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
-g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
-g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
-g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
-g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
-g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
-cd nab && make all
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-lm -lpthread
-mv dock6 ../../bin
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Wed Feb 12 10:54:21 EST 2025.
-(base) [ehspector@login2 install]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-****IMPORTANT MESSAGE BELOW****
-In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
-(base) [ehspector@login1 ~]$ home
-(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
-(base) [ehspector@login1 src]$ ls
-accessories  antechamber  dock  docktools  gbsa_grids  grid  Makefile  mopac6  rdkit  resp  tleap
-(base) [ehspector@login1 src]$ cd dock
-(base) [ehspector@login1 dock]$ ls
-amber_typer.cpp     defreal.h        iso_align.o           README                score.o
-amber_typer.h       dock.cpp         library_file.cpp      sasa.cpp              score_ph4.cpp
-amber_typer.o       dockmol.cpp      library_file.h        sasa.h                score_ph4.h
-base_grid.cpp       dockmol.h        library_file.o        sasa.o                score_ph4.o
-base_grid.h         dockmol.o        limit_max_change.cpp  score_amber.cpp       score_sasa.cpp
-base_grid.o         dock.o           limit_max_change.h    score_amber.h         score_sasa.h
-base_mpi.cpp        filter.cpp       limit_max_change.o    score_amber.o         score_sasa.o
-base_mpi.h          filter.h         lol                   score_chemgrid.cpp    score_solvent.cpp
-base_mpi.o          filter.o         Makefile              score_chemgrid.h      score_solvent.h
-base_score.cpp      fingerprint.cpp  master_conf.cpp       score_chemgrid.o      score_solvent.o
-base_score.h        fingerprint.h    master_conf.h         score.cpp             score_volume.cpp
-base_score.o        fingerprint.o    master_conf.o         score_descriptor.cpp  score_volume.h
-conf_gen_ag.cpp     fraggraph.cpp    master_score.cpp      score_descriptor.h    score_volume.o
-conf_gen_ag.h       fraggraph.h      master_score.h        score_descriptor.o    simplex.cpp
-conf_gen_ag.o       fraggraph.o      master_score.o        score_footprint.cpp   simplex.h
-conf_gen_cg.cpp     fragment.cpp     mem_info.cpp          score_footprint.h     simplex.o
-conf_gen_cg.h       fragment.h       mem_info.h            score_footprint.o     sphere.cpp
-conf_gen_cg.o       fragment.o       mem_info.o            score_gist.cpp        sphere.h
-conf_gen_dn.cpp     gasteiger.cpp    nab                   score_gist.h          sphere.o
-conf_gen_dn_ga.cpp  gasteiger.h      nabcode.h             score_gist.o          tnt
-conf_gen_dn_ga.h    gasteiger.o      nab.h                 score.h               trace.cpp
-conf_gen_dn_ga.o    grid.cpp         orient.cpp            score_hbond.cpp       trace.h
-conf_gen_dn.h       grid.h           orient.h              score_hbond.h         trace.inl
-conf_gen_dn.o       grid.o           orient.o              score_hbond.o         trace.o
-conf_gen_ga.cpp     gzstream         rddrive.cpp           score_internal.cpp    utils.cpp
-conf_gen_ga.h       hungarian.cpp    rddrive.h             score_internal.h      utils.h
-conf_gen_ga.o       hungarian.h      rddrive.o             score_internal.o      utils.o
-conf_gen_hdb.cpp    hungarian.o      rdtyper.cpp           score_multigrid.cpp   version.h
-conf_gen_hdb.h      iso_align.cpp    rdtyper.h             score_multigrid.h     xlogp.cpp
-conf_gen_hdb.o      iso_align.h      rdtyper.o             score_multigrid.o     xlogp.h
-(base) [ehspector@login1 dock]$ vi dockmol.cpp
-(base) [ehspector@login1 dock]$ cd ../../install/
-(base) [ehspector@login1 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login1 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Wed Feb 12 13:24:37 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
-g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
-g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
-g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
-g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
-g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
-g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
-g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
-g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
-g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
-g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
-g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
-g++ -c -O2 -std=c++11 -o score.o  score.cpp
-g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
-g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
-g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
-g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
-g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
-g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
-g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
-g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
-g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
-g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
-g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
-g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
-g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
-g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
-g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
-g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
-g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
-cd nab && make all
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-lm -lpthread
-mv dock6 ../../bin
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Wed Feb 12 13:27:09 EST 2025.
-(base) [ehspector@login1 install]$ cd ..
-(base) [ehspector@login1 alpha_branch]$ cd ../../4s0v/gas_teiger/
-(base) [ehspector@login1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_3.out              gas_5.out              no_charge               test_nocharge.mol2
-AAQ_yesG.mol2  gas_4.in               gas_5.out_scored.mol2  no_gas.in
-gas_2.in        gas_4.out              gas.in                 no_gas.out
-gas_2.out       gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-gas_3.in        gas_5.in               gas.out_scored.mol2    test.mol2
-(base) [ehspector@login1 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@login1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_3.out              gas_5.out              no_charge               test_nocharge.mol2
-AAQ_yesG.mol2  gas_4.in               gas_5.out_scored.mol2  no_gas.in
-gas_2.in        gas_4.out              gas.in                 no_gas.out
-gas_2.out       gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-gas_3.in        gas_5.in               gas.out_scored.mol2    test.mol2
-(base) [ehspector@login1 gas_teiger]$ vi 1AAQ_noG.mol2
-(base) [ehspector@login1 gas_teiger]$ vi gas_4.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ vi gas_3.in
-(base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2
-(base) [ehspector@login1 gas_teiger]$ vi gas_3.in
-(base) [ehspector@login1 gas_teiger]$ vi gas_3.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out
-(base) [ehspector@login1 gas_teiger]$ vi gas_3.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2
-(base) [ehspector@login1 gas_teiger]$ vi test.mol2
-(base) [ehspector@login1 gas_teiger]$ vi  gas_2.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@login1 gas_teiger]$ ls
-AAQ_noG.mol2   gas_3.out              gas_5.in               gas.out_scored.mol2     test.mol2
-AAQ_yesG.mol2  gas_3.out_scored.mol2  gas_5.out              no_charge               test_nocharge.mol2
-gas_2.in        gas_4.in               gas_5.out_scored.mol2  no_gas.in
-gas_2.out       gas_4.out              gas.in                 no_gas.out
-gas_3.in        gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ vi gas_2.in
-(base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
-(base) [ehspector@login1 gas_teiger]$ vi gas_2.out_scored.mol2
-(base) [ehspector@login1 gas_teiger]$ cd ..
-(base) [ehspector@login1 4s0v]$ cd ../../
-(base) [ehspector@login1 rizzo]$ home
-(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
-accessories/ dock/        gbsa_grids/  mopac6/      resp/
-antechamber/ docktools/   grid/        rdkit/       tleap/
-(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
-accessories/ dock/        gbsa_grids/  mopac6/      resp/
-antechamber/ docktools/   grid/        rdkit/       tleap/
-(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
-accessories/ dock/        gbsa_grids/  mopac6/      resp/
-antechamber/ docktools/   grid/        rdkit/       tleap/
-(base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@login1 dock]$ vi dockmol.cpp
-\(base) [ehspector@login1 dock]$ vi filter.cpp
-(base) [ehspector@login1 dock]$ vi library_file.cpp
-(base) [ehspector@login1 dock]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP 5EEN % ls
-een.lig.min_scored.mol2	5een_noH_nocH.mol2
-een.pdb			5een_protein_only.pdb
-een.sph			5een_surface.dms
-een_H_cH.mol2			fad_scored.mol2
-een_ligand_H_cH.mol2		flex_scored.mol2
-een_ligand_noH_nocH.mol2	rigid_scored.mol2
-een_ligand_only.pdb		selected_spheres.sph
-(base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 1O86]$ cd 005_dock/
-(base) [ehspector@milan2 005_dock]$ cd rigid/
-(base) [ehspector@milan2 rigid]$ ls
-rigid_conformers.mol2  rigid.in  rigid.out  rigid_scored.mol2  rigid.sh
-(base) [ehspector@milan2 rigid]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
-(base) [ehspector@milan2 flex]$ vi flex.out
-(base) [ehspector@milan2 flex]$ vi flex.in
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ rm flex.out
-(base) [ehspector@milan2 flex]$ bash flex.sh
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ vi flex.out
-(base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ vi flex.sh
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ ls
-flex_conformers.mol2  flex.in  flex_orients.mol2  flex.out  flex_scored.mol2  flex.sh
-(base) [ehspector@milan2 flex]$ which dock6
-/gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6
-(base) [ehspector@milan2 flex]$ vi ~/.bashrc
-(base) [ehspector@milan2 flex]$ cd ..
-(base) [ehspector@milan2 005_dock]$ cd ..
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        004_energymin          007_cartesian_min  Notes.txt
-_surface_spheres  005_dock               008_rescore        Robs_2w26
-_gridbox          006_virtual_screening  commands.txt       test4.tar
-(base) [ehspector@milan2 2w26]$ cd 004_energymin/
-(base) [ehspector@milan2 004_energymin]$ ls
-w26.lig.min_scored.mol2  min.in  min.out  min.sh
-(base) [ehspector@milan2 004_energymin]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        004_energymin          007_cartesian_min  Notes.txt
-_surface_spheres  005_dock               008_rescore        Robs_2w26
-_gridbox          006_virtual_screening  commands.txt       test4.tar
-(base) [ehspector@milan2 2w26]$ mv 006_virtual_screening/ 006_footprint
-(base) [ehspector@milan2 2w26]$ ls
-_structure        004_energymin  007_cartesian_min  Notes.txt
-_surface_spheres  005_dock       008_rescore        Robs_2w26
-_gridbox          006_footprint  commands.txt       test4.tar
-(base) [ehspector@milan2 2w26]$ cd 006_footprint/
-(base) [ehspector@milan2 006_footprint]$ touch footprint.in
-(base) [ehspector@milan2 006_footprint]$ ls
-footprint.in
-(base) [ehspector@milan2 006_footprint]$ cd ..
-(base) [ehspector@milan2 2w26]$ cp 003_gridbox/grid.sh 006_footprint/foot.sh
-(base) [ehspector@milan2 2w26]$ cd 006_footprint/
-(base) [ehspector@milan2 006_footprint]$ vi foot.sh
-(base) [ehspector@milan2 006_footprint]$ vi foot.sh
-(base) [ehspector@milan2 006_footprint]$ class
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ cd class_project/
-(base) [ehspector@milan2 class_project]$ ls
-(base) [ehspector@milan2 class_project]$ ls
-(base) [ehspector@milan2 class_project]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        004_energymin  007_cartesian_min  Notes.txt
-_surface_spheres  005_dock       008_rescore        Robs_2w26
-_gridbox          006_footprint  commands.txt       test4.tar
-(base) [ehspector@milan2 2w26]$ mv Notes.txt ../../
-(base) [ehspector@milan2 2w26]$ mv commands.txt ../../
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox    005_dock       007_cartesian_min  Robs_2w26
-_surface_spheres  004_energymin  006_footprint  008_rescore        test4.tar
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan2 AMS_536]$ vi commands.txt
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        003_gridbox    005_dock       007_cartesian_min  Robs_2w26
-_surface_spheres  004_energymin  006_footprint  008_rescore        test4.tar
-(base) [ehspector@milan2 2w26]$ mkdir 007_virtual_screen
-(base) [ehspector@milan2 2w26]$ ls
-_structure        004_energymin  007_cartesian_min   Robs_2w26
-_surface_spheres  005_dock       007_virtual_screen  test4.tar
-_gridbox          006_footprint  008_rescore
-(base) [ehspector@milan2 2w26]$ mv 007_cartesian_min/ 008_cartesian_min
-(base) [ehspector@milan2 2w26]$ mv 008_rescore/  009_rescore
-(base) [ehspector@milan2 2w26]$ cd ../5EEN/
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 5EEN]$ mv 006_virtual_screen_mpi/ 006_footprint
-(base) [ehspector@milan2 5EEN]$ mkdir 007_virtualscreen
-(base) [ehspector@milan2 5EEN]$ mv 007_cartesian_min/ 008_cartesian_min
-(base) [ehspector@milan2 5EEN]$ mv 008_rescore/ 009_rescore
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
-(base) [ehspector@milan2 5EEN]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 1O86
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_dock                007_cartesian_min  commands.txt
-_surface_spheres  004_energymin  006_virtual_screen_mpi  008_rescore
-(base) [ehspector@milan2 1O86]$ mv 006_virtual_screen_mpi/ 006_footprint
-(base) [ehspector@milan2 1O86]$ mkdir 007_virtualscreen
-(base) [ehspector@milan2 1O86]$ mv 007_cartesian_min/ 008_cartesian_min
-(base) [ehspector@milan2 1O86]$ mv 008_rescore/ 009_rescore
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ vi commands.txt
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ bash commands.txt
-commands.txt: line 2: protein_name: Is a directory
-commands.txt: line 3: protein_name: Is a directory
-commands.txt: line 4: protein_name: Is a directory
-commands.txt: line 5: protein_name: Is a directory
-commands.txt: line 6: protein_name: Is a directory
-commands.txt: line 10: protein_name: Is a directory
-commands.txt: line 11: protein_name: Is a directory
-commands.txt: line 12: protein_name: Is a directory
-commands.txt: line 13: protein_name: Is a directory
-(base) [ehspector@milan2 AMS_536]$ ls
-_dock       commands.txt  flex       protein_name  Tutorials
-class_project  fixed_anchor  Notes.txt  rigid
-(base) [ehspector@milan2 AMS_536]$ cd protein_name/
-(base) [ehspector@milan2 protein_name]$ ls
-(base) [ehspector@milan2 protein_name]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ rm protein_name/
-rm: cannot remove 'protein_name/': Is a directory
-(base) [ehspector@milan2 AMS_536]$ rm -r protein_name/
-(base) [ehspector@milan2 AMS_536]$ rm 005_dock
-(base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
-(base) [ehspector@milan2 AMS_536]$ rm -r flex/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  rigid  Tutorials
-(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ vi commands.txt
-(base) [ehspector@milan2 AMS_536]$ bash commands.txt
-(base) [ehspector@milan2 AMS_536]$ ls
-_structure        005_dock           009_rescore    flex          Tutorials
-_surface_spheres  006_footprint      class_project  Notes.txt
-_gridbox          007_virtualscreen  commands.txt   protein_name
-_energymin        008_cartesian_min  fixed_anchor   rigid
-(base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/
-(base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/
-(base) [ehspector@milan2 AMS_536]$ rm -r 003_surface_spheres/
-rm: cannot remove '003_surface_spheres/': No such file or directory
-(base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/
-(base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/
-(base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/
-(base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/
-(base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/
-(base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/
-(base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/
-(base) [ehspector@milan2 AMS_536]$ rm -r protein_name/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  fixed_anchor  flex  Notes.txt  rigid  Tutorials
-(base) [ehspector@milan2 AMS_536]$ rm -r flex
-(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
-(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
-rm: cannot remove 'rigid/': No such file or directory
-(base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
-(base) [ehspector@milan2 AMS_536]$ rm -r flex
-rm: cannot remove 'flex': No such file or directory
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ vi commands.txt
-(base) [ehspector@milan2 AMS_536]$ bash commands.txt
-mkdir: cannot create directory ‘protein_name’: File exists
-mkdir: cannot create directory ‘protein_name’: File exists
-(base) [ehspector@milan2 AMS_536]$ ls
-_structure        005_dock           009_rescore    flex          Tutorials
-_surface_spheres  006_footprint      class_project  Notes.txt
-_gridbox          007_virtualscreen  commands.txt   protein_name
-_energymin        008_cartesian_min  fixed_anchor   rigid
-(base) [ehspector@milan2 AMS_536]$ rm -r flex
-(base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
-(base) [ehspector@milan2 AMS_536]$ rm -r rigid/
-(base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/
-(base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/
-(base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/
-(base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/
-(base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/
-(base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/
-(base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/
-(base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/
-(base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  protein_name  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd protein_name/
-(base) [ehspector@milan2 protein_name]$ ls
-(base) [ehspector@milan2 protein_name]$ cd ..
-(base) [ehspector@milan2 AMS_536]$ sinfo
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      4    mix a100-[03-05,11]
-a100                      up    8:00:00      3  alloc a100-[06,08,10]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      4    mix a100-[03-05,11]
-a100-large                up    8:00:00      3  alloc a100-[06,08,10]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
-a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
-debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-debug-40core              up    1:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-extended-40core           up 7-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-extended-40core-shared    up 3-12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-extended-96core           up 7-00:00:00      1    mix dg023
-extended-96core           up 7-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-extended-96core-shared    up 3-12:00:00      1    mix dg023
-extended-96core-shared    up 3-12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
-hbm-1tb-long-96core       up 2-00:00:00      2  alloc xm[045,047]
-hbm-1tb-long-96core       up 2-00:00:00      1   idle xm046
-hbm-extended-96core       up 7-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-large-40core              up    8:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-large-96core              up    8:00:00      1    mix dg023
-large-96core              up    8:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-long-40core               up 2-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-long-40core-shared        up 1-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-long-96core               up 2-00:00:00      1    mix dg023
-long-96core               up 2-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-long-96core-shared        up 1-00:00:00      1    mix dg023
-long-96core-shared        up 1-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-medium-40core             up   12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-medium-96core             up   12:00:00      1    mix dg023
-medium-96core             up   12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-short-40core              up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-short-40core-shared       up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-short-96core              up    4:00:00      1    mix dg023
-short-96core              up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-short-96core-shared       up    4:00:00      1    mix dg023
-short-96core-shared       up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  protein_name  Tutorials
-(base) [ehspector@milan2 AMS_536]$ rm -r protein_name
-(base) [ehspector@milan2 AMS_536]$ vi ~/.bashrc
-(base) [ehspector@milan2 AMS_536]$ source ~/.bashrc
-(base) [ehspector@milan2 AMS_536]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      4    mix a100-[03-05,11]
-a100                      up    8:00:00      3  alloc a100-[06,08,10]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      4    mix a100-[03-05,11]
-a100-large                up    8:00:00      3  alloc a100-[06,08,10]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
-a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
-debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-debug-40core              up    1:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-extended-40core           up 7-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-extended-40core-shared    up 3-12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-extended-96core           up 7-00:00:00      1    mix dg023
-extended-96core           up 7-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-extended-96core-shared    up 3-12:00:00      1    mix dg023
-extended-96core-shared    up 3-12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
-hbm-1tb-long-96core       up 2-00:00:00      1  alloc xm047
-hbm-1tb-long-96core       up 2-00:00:00      2   idle xm[045-046]
-hbm-extended-96core       up 7-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00     15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-large-40core              up    8:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-large-96core              up    8:00:00      1    mix dg023
-large-96core              up    8:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-long-40core               up 2-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-long-40core-shared        up 1-00:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-long-96core               up 2-00:00:00      1    mix dg023
-long-96core               up 2-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-long-96core-shared        up 1-00:00:00      1    mix dg023
-long-96core-shared        up 1-00:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-medium-40core             up   12:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-medium-96core             up   12:00:00      1    mix dg023
-medium-96core             up   12:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-short-40core              up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      9    mix dn[001,003-005,007,018,027,051,060]
-short-40core-shared       up    4:00:00     44  alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-short-96core              up    4:00:00      1    mix dg023
-short-96core              up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00     21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
-short-96core-shared       up    4:00:00      1    mix dg023
-short-96core-shared       up    4:00:00     24  alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
-(base) [ehspector@milan2 AMS_536]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-(base) [ehspector@milan2 AMS_536]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP 5EEN % ls
-een.lig.min_scored.mol2	5een_noH_nocH.mol2
-een.pdb			5een_protein_only.pdb
-een.sph			5een_surface.dms
-een_H_cH.mol2			fad_scored.mol2
-een_ligand_H_cH.mol2		flex_scored.mol2
-een_ligand_noH_nocH.mol2	rigid_scored.mol2
-een_ligand_only.pdb		selected_spheres.sph
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ home
-(base) [ehspector@milan1 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan1 espector]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/006_footprint/
-(base) [ehspector@milan1 006_footprint]$ ls
-footprint.in  foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd
-(base) [ehspector@milan1 ~]$ cd ../../
-(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/2025/transfers/
-(base) [ehspector@milan1 transfers]$ ls
-_02_12a_test.tar
-(base) [ehspector@milan1 transfers]$ cd ..
-(base) [ehspector@milan1 2025]$ ls
-EVE_DOCK_VS  additional_files  INSPH  robbashrc_file  rotations  transfers
-(base) [ehspector@milan1 2025]$ cd transfers/
-(base) [ehspector@milan1 transfers]$ pwd
-/gpfs/projects/AMS536/2025/transfers
-(base) [ehspector@milan1 transfers]$ ^C
-(base) [ehspector@milan1 transfers]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/transfers/2025_02_12a_test.tar .
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2025_02_12a_test.tar  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ mv 2025_02_12a_test.tar 2w26/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        003_gridbox    005_dock       007_virtual_screen  009_rescore           Robs_2w26
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min   2025_02_12a_test.tar  test4.tar
-(base) [ehspector@milan1 2w26]$ tar -xf 2025_02_12a_test.tar
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   2W26
-_gridbox          006_footprint  009_rescore         Robs_2w26
-(base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan1 Robs_new_2w26]$ ls
-_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
-(base) [ehspector@milan1 005_analysis]$ ls
-fps_footprint_scored.txt      01fps_hbond_scored.txt  01fps.log1  01fps.out          01fps.sh
-fps_footprint_scored.txt.pdf  01fps.in                01fps.log2  01fps_scored.mol2
-(base) [ehspector@milan1 005_analysis]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/005_analysis/01fps.in 006_footprint/footprint.in
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/005_analysis/
-(base) [ehspector@milan1 005_analysis]$ vi 01fps
-(base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
-(base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
-(base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
-(base) [ehspector@milan1 005_analysis]$ cd ../../006_footprint/
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ vi footprint.sh
-(base) [ehspector@milan1 006_footprint]$ ls
-footprint.in  foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ cd ../001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-w26_ligand_H_cH.mol2  2w26_ligand_noH_nocH.mol2  2w26_protein_H_cH.mol2  2w26_protein_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
-Conformational Sampling Parameters
-------------------------------------------------------------------------------------------
-conformer_search_type                                        rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-use_internal_energy                                          no
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-ligand_atom_file                                             ../004_energymin/2w26.lig.min_scored.mol2
 limit_max_ligands                                            no
 skip_molecule                                                no
 read_mol_solvation                                           no
-calculate_rmsd                                               no
+calculate_rmsd                                               yes
+use_rmsd_reference_mol                                       yes
-Database Filter Parameters
+rmsd_reference_filename                                      ../004_dock/1o86_lig_min_scored.mol2
-------------------------------------------------------------------------------------------
 use_database_filter                                          no
+orient_ligand                                                yes
-Orient Ligand Parameters
+automated_matching                                           yes
-------------------------------------------------------------------------------------------
+receptor_site_file                                           ../002_surface_spheres/selected_spheres.sph
-orient_ligand                                                no
+max_orientations                                             1000
+critical_points                                              no
-Bump Filter Parameters
+chemical_matching                                            no
-------------------------------------------------------------------------------------------
+use_ligand_spheres                                           no
 bump_filter                                                  no
-Master Score Parameters
-------------------------------------------------------------------------------------------
 score_molecules                                              yes
-Contact Score Parameters
-------------------------------------------------------------------------------------------
 contact_score_primary                                        no
+grid_score_primary                                           yes
-Grid Score Parameters
+grid_score_rep_rad_scale                                     1
-------------------------------------------------------------------------------------------
+grid_score_vdw_scale                                         1
-grid_score_primary                                           no
+grid_score_es_scale                                          1
+grid_lig_efficiency                                          no
-GIST Score Parameters
+grid_score_grid_prefix                                       ../003_grid/grid
-------------------------------------------------------------------------------------------
+minimize_ligand                                              yes
-gist_score_primary                                           no
+minimize_anchor                                              yes
+minimize_flexible_growth                                     yes
-MultiGrid Score Parameters
+use_advanced_simplex_parameters                              no
-------------------------------------------------------------------------------------------
+minimize_flexible_growth_ramp                                yes
-multigrid_score_primary                                      no
+simplex_max_cycles                                           1
+simplex_score_converge                                       0.1
-Dock3.5 Score Parameters
+simplex_initial_score_coverge                                5
-------------------------------------------------------------------------------------------
+simplex_cycle_converge                                       1.0
-dock3.5_score_primary                                        no
+simplex_trans_step                                           1.0
+simplex_rot_step                                             0.1
-Continuous Energy Score Parameters
+simplex_tors_step                                            10.0
-------------------------------------------------------------------------------------------
+simplex_anchor_max_iterations                                500
-continuous_score_primary                                     no
+simplex_grow_max_iterations                                  500
+simplex_grow_tors_premin_iterations                          0
-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
+simplex_random_seed                                          0
-Atom Typing Parameters
+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
+ligand_outfile_prefix                                        flex.out
-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
-------------------------------------------------------------------------------------------
+</pre>
-Initializing Library File Routines...
-To cite Footprint Similarity Score use:
+Now, you can run the above file, flex.in, by creating a shell script (flex.sh) as stated below. This will be helpful to have if you need to re-run the job for any reason; rather than re-typing the full dock command, you can save it in the shell script file and run that script instead.
- 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
+<pre>
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+#!/bin/bash
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
------------------------------------
+dock6 -i flex.in -o flex.out
-Molecule: 2w26.pdb
+</pre>
- Elapsed time for docking:	0.008 seconds
+Now run the script-
- Anchors:		1
+<pre>
- Orientations:		1
+bash flex.sh
- Conformations:		1
+</pre>
-          Footprint_Similarity_Score:            0.761241
+DOCK6 program should finish running in a few minutes and should generate the following two files-
-                      FPS_vdw_energy:          -76.920898
+a) flex.out
-                       FPS_es_energy:           -2.930423
+b) flex_scored.mol2
-                   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
+Now we can transfer the docked files to our local system and visualize the results in chimera.
-Molecules Processed
+[[File:flex_1o86.png|600px]]
-Total elapsed time:	0.587 seconds
-Number of molecules per second:	1.705
-Virtual memory used for this process: 80220 kilobytes
-Physical memory used for this process: 8192 kilobytes
-Traceback (most recent call last):
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 9, in <module>
-    import matplotlib
-ModuleNotFoundError: No module named 'matplotlib'
-(base) [ehspector@milan1 006_footprint]$ module load python
-(base) [ehspector@milan1 006_footprint]$ module list
-Currently Loaded Modulefiles:
-) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack
-) shared                   4) mvapich2/gcc13.2/2.3.7   6) python/3.11.2
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+The docked ligand (colored in cyan) shows good structural overlap with the reference structure (purple). One way of confirming this is by looking at the RMSD value (below) which is below 1 A for this case.
+[[File:flex_param.png|600px]]
---------------------------------------
+We can also overlay the structures from the three docking types and compare with the reference to observe the best binding pose. The ligand structure obtained due to rigid docking (green)  gives the lowest RMSD score of 0.59. Next best RMSD score is obtained from flexible docking (cyan) and then from fixed anchor docking (orange), giving an RMSD of 1.27.
-DOCK v6.12
-Released September 2024
+[[File:Overlap_dock_types.png|600px]]
-Copyright UCSF
---------------------------------------
+== 007: Footprint Scoring ==
-Conformational Sampling Parameters
+Footprint analysis maps out the interaction landscape between a ligand and its target protein. By breaking down the energetics of binding into electrostatic and van der Waals (VDW) contributions, it provides a detailed visualization of how different parts of a ligand interact with specific regions of the protein.
-------------------------------------------------------------------------------------------
-conformer_search_type                                        rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-use_internal_energy                                          no
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-ligand_atom_file                                             ../004_energymin/2w26.lig.min_scored.mol2
-limit_max_ligands                                            no
-skip_molecule                                                no
-read_mol_solvation                                           no
-calculate_rmsd                                               no
-Database Filter Parameters
-------------------------------------------------------------------------------------------
-use_database_filter                                          no
-Orient Ligand Parameters
-------------------------------------------------------------------------------------------
-orient_ligand                                                no
-Bump Filter Parameters
-------------------------------------------------------------------------------------------
-bump_filter                                                  no
-Master Score Parameters
-------------------------------------------------------------------------------------------
-score_molecules                                              yes
-Contact Score Parameters
-------------------------------------------------------------------------------------------
-contact_score_primary                                        no
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-grid_score_primary                                           no
-GIST Score Parameters
-------------------------------------------------------------------------------------------
-gist_score_primary                                           no
-MultiGrid Score Parameters
-------------------------------------------------------------------------------------------
-multigrid_score_primary                                      no
-Dock3.5 Score Parameters
-------------------------------------------------------------------------------------------
-dock3.5_score_primary                                        no
-Continuous Energy Score Parameters
-------------------------------------------------------------------------------------------
-continuous_score_primary                                     no
-Footprint Similarity Score Parameters
-------------------------------------------------------------------------------------------
-footprint_similarity_score_primary                           yes
-fps_score_use_footprint_reference_mol2                       yes
-fps_score_footprint_reference_mol2_filename                  ../001_structure/2w26_ligand_H_cH.mol2
-fps_score_foot_compare_type                                  Euclidean
--------------------------------------------------------------
-You chose to use the Euclidean distance as the metric
-to compare the footprints.  When the value is 0 then
-there is perfect agreement between the two footprints.
-As the agreement gets worse between the two
-footprints the value increases.
--------------------------------------------------------------
-fps_score_normalize_foot                                     no
-fps_score_foot_comp_all_residue                              yes
-fps_score_receptor_filename                                  ../001_structure/2w26_protein_H_cH.mol2
-fps_score_vdw_att_exp                                        6
-fps_score_vdw_rep_exp                                        9
-fps_score_vdw_rep_rad_scale                                  1
-fps_score_use_distance_dependent_dielectric                  yes
-fps_score_dielectric                                         4.0
-fps_score_vdw_fp_scale                                       1
-fps_score_es_fp_scale                                        1
-fps_score_hb_fp_scale                                        0
-Pharmacophore Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
-------------------------------------------------------------------------------------------
-minimize_ligand                                              no
-simplex_final_min                                            no
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-atom_model                                                   all
-vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
-flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-ligand_outfile_prefix                                        footprint
-write_mol_solvation                                          no
-write_footprints                                             yes
-write_hbonds                                                 yes
-write_orientations                                           no
-num_scored_conformers                                        1
-score_threshold                                              100.0
-rank_ligands                                                 no
-------------------------------------------------------------------------------------------
-Initializing Library File Routines...
-To cite Footprint Similarity Score use:
- Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
------------------------------------
-Molecule: 2w26.pdb
- Elapsed time for docking:	0.008 seconds
- Anchors:		1
- Orientations:		1
- Conformations:		1
-          Footprint_Similarity_Score:            0.761241
-                      FPS_vdw_energy:          -76.920898
-                       FPS_es_energy:           -2.930423
-                   FPS_vdw+es_energy:          -79.851318
-                       FPS_num_hbond:                   2
-                         FPS_vdw_fps:            0.642335
-                          FPS_es_fps:            0.118906
-                          FPS_hb_fps:            0.000000
-                   FPS_vdw_fp_numres:                 286
-                    FPS_es_fp_numres:                 286
-                    FPS_hb_fp_numres:                 286
-Molecules Processed
-Total elapsed time:	0.487 seconds
-Number of molecules per second:	2.053
-Virtual memory used for this process: 80224 kilobytes
-Physical memory used for this process: 8192 kilobytes
-Traceback (most recent call last):
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
-    main()
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
-    (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
-                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
-    fp_file = open(filename,'r')
-              ^^^^^^^^^^^^^^^^^^
-FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt'
-(base) [ehspector@milan1 006_footprint]$ ls
-footprint_footprint_scored.txt  footprint_hbond_scored.txt  footprint.in  footprint_scored.mol2  foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
+Move to your <~/tutorial/007_footprint</code> directory and create an input file (fps.in).
+<pre>
+vi fps.in
+</pre>
-Conformational Sampling Parameters
+Add the following-
-------------------------------------------------------------------------------------------
+<pre>
 conformer_search_type                                        rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
 use_internal_energy                                          no
+ligand_atom_file                                             ../004_dock/1O86_min_scored.mol2
-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_footprint_reference_mol2_filename                  ../001_structure/1O86_ligand_wH_wcH.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_receptor_filename                                  ../001_structure/1O86_protein_wH_wcH.mol2
 fps_score_vdw_att_exp                                        6
 fps_score_vdw_rep_exp                                        9
@@ Line 13,075: / Line 745: @@
 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
+ligand_outfile_prefix                                        fps
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-ligand_outfile_prefix                                        2w26
 write_mol_solvation                                          no
 write_footprints                                             yes
@@ Line 13,122: / Line 759: @@
 score_threshold                                              100.0
 rank_ligands                                                 no
-------------------------------------------------------------------------------------------
-Initializing Library File Routines...
-To cite Footprint Similarity Score use:
+</pre>
- 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
+Now create a bash script to run the above create file-
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+<pre>
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+vi fps.sh
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
+</pre>
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
------------------------------------
+<pre>
-Molecule: 2w26.pdb
+#!/bin/bash
- Elapsed time for docking:	0.008 seconds
+echo "Running DOCK for footprint generation..."
- Anchors:		1
+dock6 -i fps.in -o fps.out >&fps.log1
- Orientations:		1
- Conformations:		1
-          Footprint_Similarity_Score:            0.761241
+echo "Generating plot..."
-                      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
+python /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py fps_footprint_scored.txt  50 >&fps.log2
-Molecules Processed
+echo "Done"
-Total elapsed time:	0.525 seconds
+</pre>
-Number of molecules per second:	1.905
-Virtual memory used for this process: 80224 kilobytes
-Physical memory used for this process: 8192 kilobytes
-Traceback (most recent call last):
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
-    main()
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
-    (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
-                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
-    fp_file = open(filename,'r')
-              ^^^^^^^^^^^^^^^^^^
-FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt'
-(base) [ehspector@milan1 006_footprint]$ ls
-w26_footprint_scored.txt  footprint_footprint_scored.txt  footprint_scored.mol2
-w26_hbond_scored.txt      footprint_hbond_scored.txt      foot.sh
-w26_scored.mol2           footprint.in
-(base) [ehspector@milan1 006_footprint]$ rm *mol2
-(base) [ehspector@milan1 006_footprint]$ ls
-w26_footprint_scored.txt  footprint_footprint_scored.txt  footprint.in
-w26_hbond_scored.txt      footprint_hbond_scored.txt      foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ rm *.txt
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+As shown above, the .sh script also includes the path to a python file that generates and saves the footprint analysis results as a PDF. Once the script has been executed, transfer the generated PDF to your local system to review the results. The output should resemble the example shown below, showing a visual representation of the electrostatic and van der Waals interactions between the ligand and the protein.
+[[File:Footprint_score_1o86.png|600px]]
---------------------------------------
+== 008: 5K Virtual Screening ==
-DOCK v6.12
-Released September 2024
+In this section, you will conduct a virtual screening on a set of druglike potential leads against the 1O86 receptor. Virtual screening of large ligand libraries is one of the main uses of DOCK and other molecular docking suites in drug discovery, as it allows for lead compound identification at much lower cost than traditional ''in vitro'' assays.
-Copyright UCSF
---------------------------------------
+=== Input File ===
-Conformational Sampling Parameters
+Because this section generates a high volume of molecule poses, you may need to make use of your scratch directory on Seawulf. While your home directory has a maximum storage volume of 20 gigabytes, scratch has a storage volume of 20 TERAbytes, so it will easily accommodate the output of your virtual screen. Your scratch directory should be located at <code>/gpfs/scratch/yourusername/</code>. Move there and create a directory for your virtual screening.
-------------------------------------------------------------------------------------------
-conformer_search_type                                        rigid
-Internal Energy Parameters
+Copy the input file from your <code>006_flex_dock</code> directory into your present directory. We can re-use the majority of input from this file because the docking process is the same in both cases; the only difference is in the number of molecules to be docked. If you like, you can re-name the input file using <code>mv</code> to something like <code>flex_vs.in</code> for clarity.
-------------------------------------------------------------------------------------------
-use_internal_energy                                          no
-Molecule Library Input Parameters
+The only parameter that needs to be changed in the input file is the <code>ligand_atom_file</code> parameter. Instead of the single <code>1O86_min_scored.mol2</code>, we want to dock a Mol2 file that contains multiple potential drug candidates. You should be able to find several such Mol2 files in <code>/gpfs/projects/AMS536/zzz.programs/VS_libraries/</code>. For this tutorial, we will screen the 5,000 molecule library (<code>VS_library_5K.mol2</code>), but you can elect to do the 100- (or 25,000) molecule library by simply changing the input file name. Just copy the path to the file (should be <code>/gpfs/projects/AMS536/zzz.programs/VS_libraries/VS_library_5K.mol2</code>), open the .in file, delete the current value for <code>ligand_atom_file</code>, and paste in the path. If you don't want to deal with the long filepath, you can also copy the VS_library file to your working directory, and just have the filename as the parameter instead. It is probably also advisable to change the names of other output files in the .in file so that the output is distinguishable from the previous flexible docking.
-------------------------------------------------------------------------------------------
-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
+Note that if you have moved to your scratch directory and used relative paths in the .in file for the receptor sphere file, gridbox, et cetera, those will also need to be changed to reflect your new location. Absolute paths will likely be the most efficient solution for this.
-------------------------------------------------------------------------------------------
-use_database_filter                                          no
-Orient Ligand Parameters
+=== Slurm and Job Submission ===
-------------------------------------------------------------------------------------------
-orient_ligand                                                no
-Bump Filter Parameters
+Up until this point, you have probably been running dock6 on the head node of Seawulf. This is fine for short, low-intensity jobs, like docking a single molecule or (debatably) generating a grid. However, the head node caters to all users currently accessing Seawulf, and has limited computing power at its disposal. As such, attempting to run a longer job (such as a 5,000 molecule screen) will fully consume the head node's limited resources, slowing down all user sessions in the process until the Seawulf admins notice and kick you. To safely utilize the full computing power of Seawulf, you need to submit a job to one of its allocated high-power computing nodes using its queueing system. This system tracks all jobs that have been submitted by various users and allocates them to processors as they are freed up, maximizing the productivity and efficiency of the computing cluster while ensuring a smooth user experience. The system Seawulf uses for this queue tracking is called Slurm (Simple Linux Utility and Resource Management).
-------------------------------------------------------------------------------------------
-bump_filter                                                  no
-Master Score Parameters
+Slurm is implemented as a ''module'' on Seawulf, and needs to be loaded into your environment before it can be used. You can load it by typing <code>module load slurm</code> into your terminal from any directory. Of note, you will need to do this every time you start a new SSH session. If you want the module to always be loaded when you log in, you can add the command to your .bashrc file (see section 000 for instructions on how to modify your .bashrc).
-------------------------------------------------------------------------------------------
-score_molecules                                              yes
-Contact Score Parameters
+Once the module has loaded, you can use the command <code>sinfo</code> to view what processors are present on Seawulf. If you are on Milan, you should see 40- and 96-core queues of varying lengths (short, medium, long), as well as some specialized GPU cores and high memory cores. The [https://rci.stonybrook.edu/HPC/faqs/seawulf-queues Seawulf website] has some good descriptions of what cores are available and the duration of jobs allowed on them. <code>sinfo --state=idle</code> allows you to see what queues have cores idle; this is helpful for knowing where a job can start running immediately.
-------------------------------------------------------------------------------------------
-contact_score_primary                                        no
-Grid Score Parameters
+To submit a job to a queue, you need to create a special job script file that will tell the queue everything it needs to know about the job, as well as what commands to run. Here is what that file will look like for our VS run:
-------------------------------------------------------------------------------------------
-grid_score_primary                                           no
-GIST Score Parameters
+ <nowiki>
-------------------------------------------------------------------------------------------
+#!/bin/bash
-gist_score_primary                                           no
+#
+#SBATCH --job-name=1o86_vs
+#SBATCH --output=vs_output.txt
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=96
+#SBATCH --time=48:00:00
+#SBATCH -p long-96core
-MultiGrid Score Parameters
+module load intel/mpi/64/2018/18.0.3
-------------------------------------------------------------------------------------------
-multigrid_score_primary                                      no
-Dock3.5 Score Parameters
+mpirun -np 96 dock6.mpi -i flex_vs.in -o flex_vs.out
-------------------------------------------------------------------------------------------
+</nowiki>
-dock3.5_score_primary                                        no
-Continuous Energy Score Parameters
+A line-by-line breakdown of this file:
-------------------------------------------------------------------------------------------
+* <code>#!/bin/bash</code> is called a shebang, and is used in unix shell scripts to indicate that bash should be used to interpret and execute the script.
-continuous_score_primary                                     no
+* <code>#SBATCH --job-name=1O86_vs</code> tells slurm what our job is called; this can be changed to whatever strikes your fancy without consequence
+* <code>#SBATCH --output=vs_output.txt</code> tells slurm where to output information about the job itself. If jobs are not running properly, check this file for errors.
+* <code>#SBATCH --nodes=1</code> tells slurm how many computing nodes we want for this job. 1 is appropriate here because we are not using any parallel processing functionality.
+* <code>#SBATCH --ntasks-per-node=96</code> tells slurm how many tasks it should expect to run per node. There are no strict guidelines on this, but setting it equal to the number of cores in the node (96 or 40 on Milan) is a good default.
+* <code>#SBATCH --time=48:00:00</code> tells slurm the maximum amount of time it should allocate for this job. The best thing to do here is request the maximum time possible for the queue; check the [https://rci.stonybrook.edu/HPC/faqs/seawulf-queues Seawulf website] for each queue's parameters. Here, because we are submitting to the long-96core queue, we are requesting the queue maximum of 48 hours; our job will likely not take that long.
+* <code>#SBATCH -p long-96core</code> tells slurm which queue we would like to submit to; in this case, we are submitting to the long-term 96-core queue.
+* <code>module load intel/mpi/64/2018/18.0.3</code> loads a module that allows for parallel processing, greatly speeding up job progress.
+* <code>mpirun -np 96 dock6.mpi -i flex_vs.in -o flex_vs.out</code> is the actual command we would like to run in the job. This particular command asks <code>mpirun</code>, which implements parallel processing, to run the MPI version of dock6 for our screening. The <code>np</code> parameter provides information on the number of processors available for MPI; this can be calculated by multiplying <code>nodes</code> by <code>ntasks-per-node</code> (96 * 1 in this case).
-Footprint Similarity Score Parameters
+Now that you have a sense of what we're trying to do, create a shell file with a recognizable name (ex, job.sh) and either copy-paste or re-type the above input into the file, making any modifications to the dock path or input filename as needed. Save and exit the file.
-------------------------------------------------------------------------------------------
-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
+Finally, you are ready to submit your first job to the queue. Use the command <code>sbatch job.sh</code> to submit your job file. If slurm accepts it, you will be provided a job number.
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
+[[File:JobSubmitted.png|600px]]
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
+You can use the command <code>squeue -u yourusername</code> to check the status of your job. If you do not see it in the queue directly after submitting, it has likely encountered an error, and you will need to troubleshoot. A good place to start will be reading any generated output files.
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
+[[File:JobRunning.png|600px]]
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
+Otherwise, it will likely start as PD (pending) for a time (depending on how full the queue is, this can vary from a minute to a day. Sorry.) before switching to R (running). As it runs, you should see .mol2 files spontaneously created in the directory. Make sure to check semi-regularly that the job is still running.
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
+Once the virtual screen has finished, you should have a .mol2 file in your directory that contains the best poses of the 5,000 ligands that were screened, according to purely grid-based docking.
-------------------------------------------------------------------------------------------
-SASA Score Parameters
+=== Re-scoring Docked Molecules ===
-------------------------------------------------------------------------------------------
-Amber Score Parameters
+Although grid scoring provides a good initial look at the most favorable poses of the given molecules, it is generally a good idea to re-score the poses provided by a different criteria to determine a final order. In this case, we will use footprint similarity scoring (FPS) as our re-scoring function. Once again, we can copy the input file that we used in the single-molecule footprint scoring example, and change the <code>ligand_atom_file</code> parameter from the 1O86 ligand to the output poses from the virtual screening. You should also change <code>ranked_ligands</code> to <code>yes</code> (towards the end of the file), and add a line with the parameter <code>max_ranked_ligands</code> set to <code>500</code> at the end of the file. This will ensure that the final .mol2 is a manageable size, while retaining the best poses of the docking. Finally, set the <code>ligand_outfile_prefix</code> parameter to something that will distinguish it from the other output already in the directory. Write and exit the file, and rename it to something appropriate like <code>rescore.in</code>.
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
+Because this re-scoring uses rigid docking and no grid calculations, it should be relatively lightweight and safe to run on the head node. If you want to be safe (or if it is still running after a couple minutes), you can cancel it and use the command <code>srun -p short-96core -t 1:00:00 --pty bash</code> to instead open up an interactive bash session on one of the computing nodes. This will let you use an interactive terminal in a manner identical to the head node, but direct all processing requests to an available computing node instead of using the head node's resources. Unfortunately, it is also subject to the whims of the queue availability, so you may have to wait a while or time strategically to obtain an available node.
-------------------------------------------------------------------------------------------
-minimize_ligand                                              no
-simplex_final_min                                            no
-Atom Typing Parameters
+Once you run the re-scoring using <code> dock6 -i rescore.in -o rescore.out</code>, you should see a re-scored ligand file in the directory with the prefix indicated in the rescore.in file. If you want, you can copy this .mol2 file to your home directory so that it is not purged after 30 days (a convenient feature of the scratch directory). After that, download it to your local machine using <code>scp</code>.
-------------------------------------------------------------------------------------------
-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
+=== Viewing VS Results in Chimera ===
-------------------------------------------------------------------------------------------
-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:
+Thanks to our infallible foresight, we have saved only the 500 best ligands to visualize in Chimera, as opposed to the original, crash-inducing number of 5,000. To analyze the poses of these ligands, launch Chimera and File >> Open your receptor .mol2 file. Then, navigate to Tools >> Surface/Binding Analysis >> ViewDock, and open the 500-ligand .mol2 file that you have just downloaded. Chimera may lag for a minute depending on your system specs, but should eventually provide a dialogue box and display one ligand in (hopefully) your receptor's binding site.
- 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
+[[File:VS ViewDock.png|600px]]
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
-Warning: atom type Ca in Fingerprint::return_atom_type not recognized
------------------------------------
+The dialogue box allows you to select one or multiple ligands at a time to view, and displays their scores in a nice table format. You can view additional columns of data in the dialogue box by navigating to Column >> Show and selecting the desired parameter, and view multiple ligands at a time by clicking one, then holding shift and clicking another.
-Molecule: 2w26.pdb
- Elapsed time for docking:	0.008 seconds
+Congratulations! You have successfully conducted a virtual screening, learned how to use slurm in the process, and now have results for potential lead compounds targeting this receptor.
- Anchors:		1
+== 009: Genetic Algorithm ==
- Orientations:		1
- Conformations:		1
-          Footprint_Similarity_Score:            0.761241
+In addition to providing a platform for traditional virtual screening methods, DOCK also implements several unique algorithms for ''de novo''-type drug design. One of these is the genetic algorithm (GA), which accepts one or several "parent" molecules and "mutates" them with basic substitutions, insertions, or deletions using a standard molecular fragment library before culling the resultant "population" based on user-specified metrics. The intent is to iteratively improve molecules over several "generations" of mutation-cull steps so that new chemical space can be explored, and more potent ligands found.
-                      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
+In order for the GA to mutate the provided parent molecules, it needs a standard library of molecular fragments to draw from. DOCK provides a foundational library that is generally effective in most GA applications, but can also accept .mol2 files to fragment and use as a custom library. To make this tutorial as educational as possible, you will learn how to fragment a molecule and add it to the foundational fragment library before running the genetic algorithm.
-Molecules Processed
+First, move to your <code>009_gen_alg</code> directory and create a directory within it called <code>fraglib/</code>. Then, move into that directory in preparation for creating the fraglib generation input file.
-Total elapsed time:	0.585 seconds
-Number of molecules per second:	1.710
-Virtual memory used for this process: 80224 kilobytes
-Physical memory used for this process: 8192 kilobytes
-No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
-/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
-  plt.show()
-(base) [ehspector@milan1 006_footprint]$ ls
-w26_footprint_scored.txt      2w26_hbond_scored.txt  footprint.in
-w26_footprint_scored.txt.pdf  2w26_scored.mol2       foot.sh
-(base) [ehspector@milan1 006_footprint]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan1 Robs_new_2w26]$ ls
-_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
-(base) [ehspector@milan1 005_analysis]$ ls
-fps_footprint_scored.txt      01fps_hbond_scored.txt  01fps.log1  01fps.out          01fps.sh
-fps_footprint_scored.txt.pdf  01fps.in                01fps.log2  01fps_scored.mol2
-(base) [ehspector@milan1 005_analysis]$ cd ../006_ga_lib/
-(base) [ehspector@milan1 006_ga_lib]$ ls
-lib.sh                  2W26.fraglib.out             2W26_fragout_scored.mol2
-combine.sh              2W26_fraglib_rigid.mol2      full_fraglib.dat
-W26.fraglib.in           2W26_fraglib_scaffold.mol2   full_sorted_fraglib.dat
-W26_fraglib_linker.mol2  2W26_fraglib_sidechain.mol2  unique_full_sorted_fraglib.dat
-W26.fraglib.log          2W26_fraglib_torenv.dat
-(base) [ehspector@milan1 006_ga_lib]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan1 Robs_new_2w26]$ ls
-_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 000_test/
-(base) [ehspector@milan1 000_test]$ ls
-test_dock.in
-(base) [ehspector@milan1 000_test]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/
-(base) [ehspector@milan1 004_dock]$ ls
-min.in           02rgd.in           03fad.in           04flx.in   05vs.out
-min.log          02rgd.log          03fad.log          04flx.log  05vs_scored.mol2
-min.out          02rgd.out          03fad.out          04flx.out  05vs.sh
-min_scored.mol2  02rgd_scored.mol2  03fad_scored.mol2  04flx.sh   05vs_slurm
-min.sh           02rgd.sh           03fad.sh           05vs.in    VS_library_005.mol2
-(base) [ehspector@milan1 004_dock]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/004_dock/05vs.in 007_virtual_screen/
-(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-vs.in
-(base) [ehspector@milan1 007_virtual_screen]$ mv 05vs.in virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ cd
-(base) [ehspector@milan1 ~]$ cd ../../
-(base) [ehspector@milan1 gpfs]$ cd AMS536
--bash: cd: AMS536: No such file or directory
-(base) [ehspector@milan1 gpfs]$ cd projects/AMS536
-(base) [ehspector@milan1 AMS536]$ ls
-EVE_Lig_nH.mol2    1eve_Rec_nH.mol2  2018  2021  2024            junk.txt
-EVE_Lig_wH.mol2    1eve_Rec_wH.mol2  2019  2022  2025            zzz.anchors
-EVE_Rec_nHDMS.dms  2017              2020  2023  get_anchors.py  zzz.programs
-(base) [ehspector@milan1 AMS536]$ cd 2025
-(base) [ehspector@milan1 2025]$ cd ..
-(base) [ehspector@milan1 AMS536]$ cd zzz.programs/
-(base) [ehspector@milan1 zzz.programs]$ ls
-amber16          dock6.11         dock6-master.zip     plot_footprint_single_magnitude.py
-de_novo_anchors  dock6.11_alpha   dock_directory_arch  plot_rmsds_amber
-dock6.10         dock6.12         gen-frags-12         VS_libraries
-dock6.10_milan   dock6.12_ams536  old
-(base) [ehspector@milan1 zzz.programs]$ cd VS_libraries/
-(base) [ehspector@milan1 VS_libraries]$ ls
-VS_library_100.mol2  VS_library_25K.mol2  VS_library_5K.mol2
-(base) [ehspector@milan1 VS_libraries]$ pwd
-/gpfs/projects/AMS536/zzz.programs/VS_libraries
-(base) [ehspector@milan1 VS_libraries]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ cd ../006_footprint/
-(base) [ehspector@milan1 006_footprint]$ ls
-w26_footprint_scored.txt      2w26_hbond_scored.txt  footprint.in
-w26_footprint_scored.txt.pdf  2w26_scored.mol2       foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ cd ../007_virtual_screen/
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
-(base) [ehspector@milan1 007_virtual_screen]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan1 Robs_new_2w26]$ ls
-_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
-(base) [ehspector@milan1 005_analysis]$ ls
-fps_footprint_scored.txt      01fps_hbond_scored.txt  01fps.log1  01fps.out          01fps.sh
-fps_footprint_scored.txt.pdf  01fps.in                01fps.log2  01fps_scored.mol2
-(base) [ehspector@milan1 005_analysis]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/
-(base) [ehspector@milan1 004_dock]$ ls
-min.in           02rgd.in           03fad.in           04flx.in   05vs.out
-min.log          02rgd.log          03fad.log          04flx.log  05vs_scored.mol2
-min.out          02rgd.out          03fad.out          04flx.out  05vs.sh
-min_scored.mol2  02rgd_scored.mol2  03fad_scored.mol2  04flx.sh   05vs_slurm
-min.sh           02rgd.sh           03fad.sh           05vs.in    VS_library_005.mol2
-(base) [ehspector@milan1 004_dock]$ vi 05vs.sh
-(base) [ehspector@milan1 004_dock]$ vi 05vs.sh
-(base) [ehspector@milan1 004_dock]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-virtual.in  virtual.slurm
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
-(base) [ehspector@milan1 007_virtual_screen]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      4    mix a100-[03-05,11]
-a100                      up    8:00:00      3  alloc a100-[06,08,10]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      4    mix a100-[03-05,11]
-a100-large                up    8:00:00      3  alloc a100-[06,08,10]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
-a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
-debug-40core              up    1:00:00      3   plnd dn[032,040,049]
-debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      8    mix dn[001,003-005,007,018,027,051]
-debug-40core              up    1:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-extended-40core           up 7-00:00:00      3   plnd dn[032,040,049]
-extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      8    mix dn[001,003-005,007,018,027,051]
-extended-40core           up 7-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-extended-40core-shared    up 3-12:00:00      3   plnd dn[032,040,049]
-extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      8    mix dn[001,003-005,007,018,027,051]
-extended-40core-shared    up 3-12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-extended-96core           up 7-00:00:00      1    mix dg023
-extended-96core           up 7-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-extended-96core-shared    up 3-12:00:00      1    mix dg023
-extended-96core-shared    up 3-12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
-hbm-1tb-long-96core       up 2-00:00:00      1  alloc xm045
-hbm-1tb-long-96core       up 2-00:00:00      2   idle xm[046-047]
-hbm-extended-96core       up 7-00:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00     14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     75  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      3   plnd dn[032,040,049]
-large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      8    mix dn[001,003-005,007,018,027,051]
-large-40core              up    8:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-large-96core              up    8:00:00      1    mix dg023
-large-96core              up    8:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-long-40core               up 2-00:00:00      3   plnd dn[032,040,049]
-long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      8    mix dn[001,003-005,007,018,027,051]
-long-40core               up 2-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-long-40core-shared        up 1-00:00:00      3   plnd dn[032,040,049]
-long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      8    mix dn[001,003-005,007,018,027,051]
-long-40core-shared        up 1-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-long-96core               up 2-00:00:00      1    mix dg023
-long-96core               up 2-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-long-96core-shared        up 1-00:00:00      1    mix dg023
-long-96core-shared        up 1-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-medium-40core             up   12:00:00      3   plnd dn[032,040,049]
-medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      8    mix dn[001,003-005,007,018,027,051]
-medium-40core             up   12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-medium-96core             up   12:00:00      1    mix dg023
-medium-96core             up   12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-ood-short-96core          up    4:00:00      1  alloc dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      3   plnd dn[032,040,049]
-short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
-short-40core              up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-short-40core-shared       up    4:00:00      3   plnd dn[032,040,049]
-short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
-short-40core-shared       up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-short-96core              up    4:00:00      1    mix dg023
-short-96core              up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-short-96core-shared       up    4:00:00      1    mix dg023
-short-96core-shared       up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-virtual.in  virtual.slurm
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
-(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.slurm
-sbatch: error: QOSMaxNodePerJobLimit
-sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
-(base) [ehspector@milan1 007_virtual_screen]$ mv virtual.slurm virtual.sh
-(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
-sbatch: error: QOSMaxNodePerJobLimit
-sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
-Submitted batch job 927425
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan1 007_virtual_screen]$
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan1 007_virtual_screen]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+=== Generating Fragments ===
-. Duo Push to XXX-XXX-9204
+The overall goal in this section is to use DOCK to fragment the ligand present in the 1O86 system, and add those fragments to the foundational library. The backbone of this operation is the <code>write_fragment_libraries</code> option in the DOCK input file. Below is what a sample input file would look like; you may copy and paste it directly, but we recommend moving through DOCK's decision tree and understanding what defaults the program has that we are changing. In this instance, we override several defaults such as <code>orient_ligand</code> and <code>score_molecule</code>, as these are unnecessary for the pure operation of generating ligand fragments. We will refer to the input file as <code>fraglib_gen.in</code> Some parameters are left as exercises to the reader; refer back to previous steps if confused.
-Passcode or option (1-1): 1
+ <nowiki>
+conformer_search_type                                    	flex
+write_fragment_libraries                                 	yes
+fragment_library_prefix                                  	1O86_lig_fraglib
+fragment_library_freq_cutoff                             	1
+fragment_library_sort_method                             	freq
+fragment_library_trans_origin                            	no
+use_internal_energy                                      	no
+ligand_atom_file                                         	FILL IN 1O86 LIGAND MOL2
+limit_max_ligands                                        	no
+skip_molecule                                            	no
+read_mol_solvation                                       	no
+calculate_rmsd                                           	no
+use_database_filter                                      	no
+orient_ligand                                            	no
+bump_filter                                              	no
+score_molecules                                          	no
+atom_model                                               	all
+vdw_defn_file                                            	FILL IN VDW.DEFN FILEPATH
+flex_defn_file                                           	FILL IN FLEX.DEFN FILEPATH
+flex_drive_file                                          	FILL IN FLEX_DRIVE FILEPATH
+ligand_outfile_prefix                                    	1o86_fraglib
+write_mol_solvation                                      	no
+write_orientations                                       	no
+num_scored_conformers                                    	1
+score_threshold                                          	100.0
+rank_ligands                                             	no
+</nowiki>
-Pushed a login request to your device...
+Once you have created this input file and inserted the relevant filepaths, you can run DOCK to generate the fragments:
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan1 ~]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      4    mix a100-[03-05,11]
-a100                      up    8:00:00      3  alloc a100-[06,08,10]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      4    mix a100-[03-05,11]
-a100-large                up    8:00:00      3  alloc a100-[06,08,10]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      4    mix a100-[03-05,11]
-a100-long                 up 2-00:00:00      3  alloc a100-[06,08,10]
-debug-40core              up    1:00:00      3   plnd dn[032,040,049]
-debug-40core              up    1:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      8    mix dn[001,003-005,007,018,027,051]
-debug-40core              up    1:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-extended-40core           up 7-00:00:00      3   plnd dn[032,040,049]
-extended-40core           up 7-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      8    mix dn[001,003-005,007,018,027,051]
-extended-40core           up 7-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-extended-40core-shared    up 3-12:00:00      3   plnd dn[032,040,049]
-extended-40core-shared    up 3-12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      8    mix dn[001,003-005,007,018,027,051]
-extended-40core-shared    up 3-12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-extended-96core           up 7-00:00:00      1    mix dg023
-extended-96core           up 7-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-extended-96core-shared    up 3-12:00:00      1    mix dg023
-extended-96core-shared    up 3-12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-hbm-1tb-long-96core       up 2-00:00:00      1 alloc@ xm048
-hbm-1tb-long-96core       up 2-00:00:00      1  alloc xm045
-hbm-1tb-long-96core       up 2-00:00:00      2   idle xm[046-047]
-hbm-extended-96core       up 7-00:00:00      2   plnd xm[008,094]
-hbm-extended-96core       up 7-00:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
-hbm-large-96core          up    8:00:00      2   plnd xm[008,094]
-hbm-large-96core          up    8:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
-hbm-long-96core           up 2-00:00:00      2   plnd xm[008,094]
-hbm-long-96core           up 2-00:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
-hbm-medium-96core         up   12:00:00      2   plnd xm[008,094]
-hbm-medium-96core         up   12:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
-hbm-short-96core          up    4:00:00      2   plnd xm[008,094]
-hbm-short-96core          up    4:00:00     13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     74  alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
-large-40core              up    8:00:00      3   plnd dn[032,040,049]
-large-40core              up    8:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      8    mix dn[001,003-005,007,018,027,051]
-large-40core              up    8:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-large-96core              up    8:00:00      1    mix dg023
-large-96core              up    8:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-long-40core               up 2-00:00:00      3   plnd dn[032,040,049]
-long-40core               up 2-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      8    mix dn[001,003-005,007,018,027,051]
-long-40core               up 2-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-long-40core-shared        up 1-00:00:00      3   plnd dn[032,040,049]
-long-40core-shared        up 1-00:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      8    mix dn[001,003-005,007,018,027,051]
-long-40core-shared        up 1-00:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-long-96core               up 2-00:00:00      1    mix dg023
-long-96core               up 2-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-long-96core-shared        up 1-00:00:00      1    mix dg023
-long-96core-shared        up 1-00:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-medium-40core             up   12:00:00      3   plnd dn[032,040,049]
-medium-40core             up   12:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      8    mix dn[001,003-005,007,018,027,051]
-medium-40core             up   12:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-medium-96core             up   12:00:00      1    mix dg023
-medium-96core             up   12:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      3   plnd dn[032,040,049]
-short-40core              up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
-short-40core              up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-short-40core-shared       up    4:00:00      3   plnd dn[032,040,049]
-short-40core-shared       up    4:00:00      7 alloc@ dn[009,026,029,033,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      8    mix dn[001,003-005,007,018,027,051]
-short-40core-shared       up    4:00:00     42  alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-short-96core              up    4:00:00      1    mix dg023
-short-96core              up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00     16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
-short-96core-shared       up    4:00:00      1    mix dg023
-short-96core-shared       up    4:00:00     29  alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
-(base) [ehspector@milan1 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan1 2w26]$ scancel 927425
-(base) [ehspector@milan1 2w26]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-virtual.in  virtual.sh
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
-Submitted batch job 927435
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 007_virtual_screen]$ cd ..
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 5EEN/006_footprint/footprint.in
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 5EEN/006_footprint/foot.sh
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 1O86/006_footprint/foot.sh
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 1O86/006_footprint/footprint.in
-(base) [ehspector@milan1 Tutorials]$ cd 5EEN/006_footprint/
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ module load python
-(base) [ehspector@milan1 006_footprint]$ cd ../001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-een_H_cH.mol2  5een_ligand_H_cH.mol2  5een_ligand_noH_nocH.mol2  5een_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
+<code>dock6 -i fraglib_gen.in -o fraglib_gen.out</code>
+Because we are only fragmenting one molecule, this program should be fine to run on the head node, and should finish in a couple seconds. Once it finishes, you should see present in the directory:
+* Four .mol2 files containing "linker", "rigid", "scaffold", and "sidechain" in their names; will be referred to as <code>1o86_fraglib_TYPE.mol2</code>
+* A file ending in "torenv.dat" (referred to as 1o86_lig_torenv.dat hereafter)
+* An output_scored.mol2 file
+* A .out file with whatever name you specified
---------------------------------------
+The set of four .mol2 files contain all the fragments that DOCK was able to generate from the original molecule, and the *torenv.dat file is a record of all the torsion-able bonds that DOCK cleaved to generate the fragments.
-DOCK v6.12
-Released September 2024
+=== Combining Fragment Libraries ===
-Copyright UCSF
---------------------------------------
+Now that we have generated fragments and associated torsions from our ligand, we need to combine them with the standard DOCK fragment library and associated torsion environments. The torsion environment combination can be accomplished via a python script.
-Conformational Sampling Parameters
+First, determine the path to the default DOCK torsion environment collection. It should be located in the <code>parameters</code> folder associated with your DOCK installation. At the time of writing, the full path is <code>/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_torenv.dat</code>
-------------------------------------------------------------------------------------------
-conformer_search_type                                        rigid
-Internal Energy Parameters
+Next, determine the path for the python script used to combine torsion environments. It should be in the same <code>bin</code> directory as your dock6 command. At the time of writing, there is an instance at <code>/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/combine_torenv.py</code>
-------------------------------------------------------------------------------------------
-use_internal_energy                                          no
-Molecule Library Input Parameters
+Once you have found paths that work for both of these files, you can combine the standard torsion environment with the newly generated custom one by running
-------------------------------------------------------------------------------------------
-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
+<code>python insert_path_here/combine_torenv.py ./1o86_lig_torenv.dat insert_path_here/fraglib_torenv.dat</code>
-------------------------------------------------------------------------------------------
-use_database_filter                                          no
-Orient Ligand Parameters
+(note that you may need to use the command <code>module load python</code> if you encounter a python-related error in running this) Once the script finishes, you should have a <code>full_fraglib.dat</code>, <code>full_sorted_fraglib.dat</code> and <code>unique_full_sorted_fraglib.dat</code> files in your directory. We will be using the "unique" variant for our genetic algorithm process.
-------------------------------------------------------------------------------------------
-orient_ligand                                                no
-Bump Filter Parameters
+We also need to combine the .mol2 files that we have generated from our ligand with the standard DOCK-provided ones. Because .mol2 files just contain lists of molecules without any special header/footer text, they can just be concatenated together by a shell script. Combine the linker, scaffold, and sidechain .mol2 files with their counterparts in the <code>parameters/</code> folder using <code>cat</code>; an example would be:
-------------------------------------------------------------------------------------------
-bump_filter                                                  no
-Master Score Parameters
+<code>cat insert_path_here/parameters/fraglib_linker.mol2 ./1o86_fraglib_linker.mol2 >> combined_fraglib_linker.mol2</code>
-------------------------------------------------------------------------------------------
-score_molecules                                              yes
-Contact Score Parameters
+(Note that we do not do anything with the "rigid" .mol2; this set of fragments is not needed to run the GA). After you do this process for all three variants of the fraglib .mol2s, you will be ready to run the genetic algorithm. It may be advisable to move the ligand-specific fragment library mol2s to a sub-directory in order to prevent cluttering/confusion.
-------------------------------------------------------------------------------------------
-contact_score_primary                                        no
-Grid Score Parameters
+=== Running the GA ===
-------------------------------------------------------------------------------------------
-grid_score_primary                                           no
-GIST Score Parameters
+With all preparation completed, we can now start optimizing molecules using the genetic algorithm. We will use our original ligand as the "parent" molecule for the first generation, and allow the algorithm to mutate it into new molecules for fifty generations.
-------------------------------------------------------------------------------------------
-gist_score_primary                                           no
-MultiGrid Score Parameters
+Aside from the filepaths/filenames for the various fraglibs, ligand, protein spheres, and .defn files, the only parameters we are changing from default in the .in file are <code>ga_max_generations</code> and <code>ga_mutate_parents</code>. Maximum generations are lowered to 50 for computational tractability, and parents must be mutable because we only have one molecule to start with; the population would grow very slowly or even die off if we did not allow parental recombination. A full sample input file is given below (but as always, do please try to do it yourself):
-------------------------------------------------------------------------------------------
-multigrid_score_primary                                      no
-Dock3.5 Score Parameters
+ <nowiki>
-------------------------------------------------------------------------------------------
+conformer_search_type                                    	genetic
-dock3.5_score_primary                                        no
+ga_molecule_file                                         	ORIGINAL 1O86 LIGAND MOL2
+ga_utilities                                             	no
+ga_fraglib_scaffold_file                                 	FRAGLIB_SCAFFOLD MOL2
+ga_fraglib_linker_file                                   	FRAGLIB_LINKER MOL2
+ga_fraglib_sidechain_file                                	FRAGLIB_SIDECHAIN MOL2
+ga_torenv_table                                          	FRAGLIB TORENV DAT
+ga_max_generations                                       	50
+ga_xover_on                                              	yes
+ga_xover_sampling_method_rand                            	yes
+ga_xover_max                                             	150
+ga_bond_tolerance                                        	0.5
+ga_angle_cutoff                                          	0.14
+ga_check_overlap                                         	no
+ga_mutate_addition                                       	yes
+ga_mutate_deletion                                       	yes
+ga_mutate_substitution                                   	yes
+ga_mutate_replacement                                    	yes
+ga_mutate_parents                                        	yes
+ga_pmut_rate                                             	0.3
+ga_omut_rate                                             	0.7
+ga_max_mut_cycles                                        	5
+ga_mut_sampling_method                                   	rand
+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
+ga_selection_method                                      	elitism
+ga_elitism_combined                                      	yes
+ga_elitism_option                                        	max
+ga_max_num_gen_with_no_crossover                         	25
+ga_name_identifier                                       	1o86_ga
+ga_output_prefix                                         	1086_ga_out
+use_internal_energy                                      	yes
+internal_energy_rep_exp                                  	12
+internal_energy_cutoff                                   	100.0
+use_database_filter                                      	no
+orient_ligand                                            	yes
+automated_matching                                       	yes
+receptor_site_file                                       	RECEPTOR SPHERES .SPH
+max_orientations                                         	1000
+critical_points                                          	no
+chemical_matching                                        	no
+use_ligand_spheres                                       	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                                   	GRID PATH
+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                                            	VDW DEFN FILE
+flex_defn_file                                           	FLEX DEFN FILE
+flex_drive_file                                          	FLEX_DRIVE FILE
+</nowiki>
-Continuous Energy Score Parameters
+We will also need to create a batch file to run the GA using slurm, as it is an intensive process that will take a number of hours to run. A sample is provided below; you should adopt yours to the appropriate queue, job name, time to run, DOCK path, and input filename:
-------------------------------------------------------------------------------------------
-continuous_score_primary                                     no
-Footprint Similarity Score Parameters
+ <nowiki>
-------------------------------------------------------------------------------------------
+#!/bin/bash
-footprint_similarity_score_primary                           yes
+#
-fps_score_use_footprint_reference_mol2                       yes
+#SBATCH --job-name=1o86_GA
-fps_score_footprint_reference_mol2_filename                  ../001_structure/5een_ligand_H_cH.mol2
+#SBATCH --output=ga_output.txt
-fps_score_foot_compare_type                                  Euclidean
+#SBATCH --nodes=1
--------------------------------------------------------------
+#SBATCH --ntasks-per-node=40
-You chose to use the Euclidean distance as the metric
+#SBATCH --time=4:00:00
-to compare the footprints.  When the value is 0 then
+#SBATCH -p short-40core
-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
+change_this_to_your_path_to_dock/bin/dock6 -i genalg.in -o genalg.out
-------------------------------------------------------------------------------------------
+</nowiki>
-Hbond Energy Score Parameters
+Use <code>sbatch job.sh</code> to submit this per usual, and check up on it regularly. The first few generations should go relatively quickly, with a slowdown as the molecular population increases past generation 8-10. If you want to track the population growth, you can use <code>grep -c "Name" *mol2</code> to view the molecule populations of every .mol2 file that has been written so far.
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
+=== Analysis ===
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
+Once the genetic algorithm has finished running, you can view the final generation's best molecules and poses in Chimera via the same process outlined in section 008. To review, this will entail downloading the final .mol2 to your local machine (generation 50 in this case), launching Chimera, opening the receptor .mol2 via File >> Open, and using the Tools >> Structure/Binding Analysis >> ViewDock tool to load the ligand .mol2 file in a conveniently viewable format. An example of this can be seen below:
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
+[[File:GA_ViewDock.png|600px]]
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
+== 010: De Novo Design Example ==
-------------------------------------------------------------------------------------------
-SASA Score Parameters
+=== De Novo Design ===
-------------------------------------------------------------------------------------------
+'''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
-Amber Score Parameters
+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 [https://en.wikipedia.org/wiki/Lipinski%27s_rule_of_five Lipinski's Rule of 5]
-Simplex Minimization Parameters
+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
-minimize_ligand                                              no
+will certainly aid in enhancing your search space in generating numerous new compounds.
-simplex_final_min                                            no
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-atom_model                                                   all
-vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
-flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-ligand_outfile_prefix                                        5een
-write_mol_solvation                                          no
-write_footprints                                             yes
-write_hbonds                                                 yes
-write_orientations                                           no
-num_scored_conformers                                        1
-score_threshold                                              100.0
-rank_ligands                                                 no
-------------------------------------------------------------------------------------------
-Initializing Library File Routines...
-To cite Footprint Similarity Score use:
- Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
-Error Opening Receptor File!
-Traceback (most recent call last):
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
-    main()
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
-    (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
-                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 56, in identify_residues
-    resindex_selected.append(fp_array[(num_res-1)-i][0])
-:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])^^^^^^^^^^^^^^^
-IndexError: list index out of range
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
-Conformational Sampling Parameters
-------------------------------------------------------------------------------------------
-conformer_search_type                                        rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-use_internal_energy                                          no
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-ligand_atom_file                                             ../004_energymin/5een.lig.min_scored.mol2
-limit_max_ligands                                            no
-skip_molecule                                                no
-read_mol_solvation                                           no
-calculate_rmsd                                               no
-Database Filter Parameters
-------------------------------------------------------------------------------------------
-use_database_filter                                          no
-Orient Ligand Parameters
-------------------------------------------------------------------------------------------
-orient_ligand                                                no
-Bump Filter Parameters
-------------------------------------------------------------------------------------------
-bump_filter                                                  no
-Master Score Parameters
-------------------------------------------------------------------------------------------
-score_molecules                                              yes
-Contact Score Parameters
-------------------------------------------------------------------------------------------
-contact_score_primary                                        no
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-grid_score_primary                                           no
-GIST Score Parameters
-------------------------------------------------------------------------------------------
-gist_score_primary                                           no
-MultiGrid Score Parameters
-------------------------------------------------------------------------------------------
-multigrid_score_primary                                      no
-Dock3.5 Score Parameters
-------------------------------------------------------------------------------------------
-dock3.5_score_primary                                        no
-Continuous Energy Score Parameters
-------------------------------------------------------------------------------------------
-continuous_score_primary                                     no
-Footprint Similarity Score Parameters
-------------------------------------------------------------------------------------------
-footprint_similarity_score_primary                           yes
-fps_score_use_footprint_reference_mol2                       yes
-fps_score_footprint_reference_mol2_filename                  ../001_structure/5een_ligand_H_cH.mol2
-fps_score_foot_compare_type                                  Euclidean
--------------------------------------------------------------
-You chose to use the Euclidean distance as the metric
-to compare the footprints.  When the value is 0 then
-there is perfect agreement between the two footprints.
-As the agreement gets worse between the two
-footprints the value increases.
--------------------------------------------------------------
-fps_score_normalize_foot                                     no
-fps_score_foot_comp_all_residue                              yes
-fps_score_receptor_filename                                  ../001_structure/5een_H_cH.mol2
-fps_score_vdw_att_exp                                        6
-fps_score_vdw_rep_exp                                        9
-fps_score_vdw_rep_rad_scale                                  1
-fps_score_use_distance_dependent_dielectric                  yes
-fps_score_dielectric                                         4.0
-fps_score_vdw_fp_scale                                       1
-fps_score_es_fp_scale                                        1
-fps_score_hb_fp_scale                                        0
-Pharmacophore Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
-------------------------------------------------------------------------------------------
-Simplex Minimization Parameters
-------------------------------------------------------------------------------------------
-minimize_ligand                                              no
-simplex_final_min                                            no
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-atom_model                                                   all
-vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
-flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-ligand_outfile_prefix                                        5een
-write_mol_solvation                                          no
-write_footprints                                             yes
-write_hbonds                                                 yes
-write_orientations                                           no
-num_scored_conformers                                        1
-score_threshold                                              100.0
-rank_ligands                                                 no
-------------------------------------------------------------------------------------------
-Initializing Library File Routines...
-To cite Footprint Similarity Score use:
- Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
-WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 3018
-WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5500
-WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5501
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type K in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
------------------------------------
-Molecule: 5een.pdb
- Elapsed time for docking:	0.008 seconds
- Anchors:		1
- Orientations:		1
- Conformations:		1
-          Footprint_Similarity_Score:           10.378089
-                      FPS_vdw_energy:          -39.542568
-                       FPS_es_energy:          -11.422824
-                   FPS_vdw+es_energy:          -50.965393
-                       FPS_num_hbond:                   2
-                         FPS_vdw_fps:            8.225544
-                          FPS_es_fps:            2.152545
-                          FPS_hb_fps:            0.000000
-                   FPS_vdw_fp_numres:                 362
-                    FPS_es_fp_numres:                 362
-                    FPS_hb_fp_numres:                 362
-Molecules Processed
-Total elapsed time:	0.778 seconds
-Number of molecules per second:	1.285
-Virtual memory used for this process: 80616 kilobytes
-Physical memory used for this process: 9196 kilobytes
-No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
-/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
-  plt.show()
-(base) [ehspector@milan1 006_footprint]$ ls
-een_footprint_scored.txt      5een_hbond_scored.txt  footprint.in
-een_footprint_scored.txt.pdf  5een_scored.mol2       foot.sh
-(base) [ehspector@milan1 006_footprint]$ cd ..
-(base) [ehspector@milan1 5EEN]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd 1O86/001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-O86_ligand_H_cH.mol2  1O86_ligand_noH_nocH.mol2  1O86_protein_H_cH.mol2  1O86_protein_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
-(base) [ehspector@milan1 006_footprint]$ vi footprint.in
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ vi foot.sh
-(base) [ehspector@milan1 006_footprint]$ bash foot.sh
---------------------------------------
-DOCK v6.12
-Released September 2024
-Copyright UCSF
---------------------------------------
-Conformational Sampling Parameters
-------------------------------------------------------------------------------------------
-conformer_search_type                                        rigid
-Internal Energy Parameters
-------------------------------------------------------------------------------------------
-use_internal_energy                                          no
-Molecule Library Input Parameters
-------------------------------------------------------------------------------------------
-ligand_atom_file                                             ../004_energymin/1O86.lig.min_scored.mol2
-limit_max_ligands                                            no
-skip_molecule                                                no
-read_mol_solvation                                           no
-calculate_rmsd                                               no
-Database Filter Parameters
-------------------------------------------------------------------------------------------
-use_database_filter                                          no
-Orient Ligand Parameters
-------------------------------------------------------------------------------------------
-orient_ligand                                                no
-Bump Filter Parameters
-------------------------------------------------------------------------------------------
-bump_filter                                                  no
-Master Score Parameters
-------------------------------------------------------------------------------------------
-score_molecules                                              yes
-Contact Score Parameters
-------------------------------------------------------------------------------------------
-contact_score_primary                                        no
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-grid_score_primary                                           no
-GIST Score Parameters
-------------------------------------------------------------------------------------------
-gist_score_primary                                           no
-MultiGrid Score Parameters
-------------------------------------------------------------------------------------------
-multigrid_score_primary                                      no
-Dock3.5 Score Parameters
-------------------------------------------------------------------------------------------
-dock3.5_score_primary                                        no
-Continuous Energy Score Parameters
-------------------------------------------------------------------------------------------
-continuous_score_primary                                     no
-Footprint Similarity Score Parameters
-------------------------------------------------------------------------------------------
-footprint_similarity_score_primary                           yes
-fps_score_use_footprint_reference_mol2                       yes
-fps_score_footprint_reference_mol2_filename                  ../001_structure/1O86_ligand_H_cH.mol2
-fps_score_foot_compare_type                                  Euclidean
--------------------------------------------------------------
-You chose to use the Euclidean distance as the metric
-to compare the footprints.  When the value is 0 then
-there is perfect agreement between the two footprints.
-As the agreement gets worse between the two
-footprints the value increases.
--------------------------------------------------------------
-fps_score_normalize_foot                                     no
-fps_score_foot_comp_all_residue                              yes
-fps_score_receptor_filename                                  ../001_structure/1O86_protein_H_cH.mol2
-fps_score_vdw_att_exp                                        6
-fps_score_vdw_rep_exp                                        9
-fps_score_vdw_rep_rad_scale                                  1
-fps_score_use_distance_dependent_dielectric                  yes
-fps_score_dielectric                                         4.0
-fps_score_vdw_fp_scale                                       1
-fps_score_es_fp_scale                                        1
-fps_score_hb_fp_scale                                        0
-Pharmacophore Similarity Score Parameters
-------------------------------------------------------------------------------------------
-Hbond Energy Score Parameters
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-Hawkins GB/SA Score Parameters
-------------------------------------------------------------------------------------------
-SASA Score Parameters
-------------------------------------------------------------------------------------------
-Amber Score Parameters
+In this tutorial, you will be guided through a '''Denovo refinement calculation'''. This kind of
-------------------------------------------------------------------------------------------
+calculation involves deleting a part of a ligand, creating a dummy atom, and using the De Novo design
+algorithm to 'regrow' that part of the ligand based on user defined parameters.
+The way in which the 'regrow' process happens comes from the algorithm pulling molecules from fragment libraries
+that contain scaffolds, linkers, and sidechains. The user defined parameters will dictate which libraries the
+algorithm can pull from.
-Simplex Minimization Parameters
+The outcome will be a series of refinements that will retain a desired interaction in 1O86.
-------------------------------------------------------------------------------------------
-minimize_ligand                                              no
-simplex_final_min                                            no
-Atom Typing Parameters
-------------------------------------------------------------------------------------------
-atom_model                                                   all
-vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
-flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
-Molecule Library Output Parameters
-------------------------------------------------------------------------------------------
-ligand_outfile_prefix                                        1O86
-write_mol_solvation                                          no
-write_footprints                                             yes
-write_hbonds                                                 yes
-write_orientations                                           no
-num_scored_conformers                                        1
-score_threshold                                              100.0
-rank_ligands                                                 no
-------------------------------------------------------------------------------------------
-Initializing Library File Routines...
-To cite Footprint Similarity Score use:
- Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
-Warning: atom type Zn in Fingerprint::return_atom_type not recognized
------------------------------------
-Molecule: 1O86_ligand.pdb
- Elapsed time for docking:	0.019 seconds
- Anchors:		1
- Orientations:		1
- Conformations:		1
-          Footprint_Similarity_Score:           19.990522
-                      FPS_vdw_energy:          -62.449921
-                       FPS_es_energy:          -49.059299
-                   FPS_vdw+es_energy:         -111.509216
-                       FPS_num_hbond:                   4
-                         FPS_vdw_fps:            4.596808
-                          FPS_es_fps:           15.393714
-                          FPS_hb_fps:            1.000000
-                   FPS_vdw_fp_numres:                 582
-                    FPS_es_fp_numres:                 582
-                    FPS_hb_fp_numres:                 582
-Molecules Processed
-Total elapsed time:	2.107 seconds
-Number of molecules per second:	0.475
-Virtual memory used for this process: 83536 kilobytes
-Physical memory used for this process: 11424 kilobytes
-No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
-/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
-  plt.show()
-(base) [ehspector@milan1 006_footprint]$ ls
-O86_footprint_scored.txt      1O86_hbond_scored.txt  footprint.in
-O86_footprint_scored.txt.pdf  1O86_scored.mol2       foot.sh
-(base) [ehspector@milan1 006_footprint]$ cd ..
-(base) [ehspector@milan1 1O86]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 5EEN/007_virtualscreen/virtual.in
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 5EEN/007_virtualscreen/virtual.sh
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 1O86/007_virtualscreen/virtual.sh
-(base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 1O86/007_virtualscreen/virtual.in
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan2 ~]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      2    mix a100-[03,05]
-a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      2    mix a100-[03,05]
-a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      2    mix a100-[03,05]
-a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
-debug-40core              up    1:00:00      3   plnd dn[050,061-062]
-debug-40core              up    1:00:00      6 alloc@ dn[009,026,029,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      4    mix dn[004-005,018,051]
-debug-40core              up    1:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-extended-40core           up 7-00:00:00      3   plnd dn[050,061-062]
-extended-40core           up 7-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      4    mix dn[004-005,018,051]
-extended-40core           up 7-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-extended-40core-shared    up 3-12:00:00      3   plnd dn[050,061-062]
-extended-40core-shared    up 3-12:00:00      6 alloc@ dn[009,026,029,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      4    mix dn[004-005,018,051]
-extended-40core-shared    up 3-12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core           up 7-00:00:00      2    mix dg[009,023]
-extended-96core           up 7-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-extended-96core           up 7-00:00:00      3   idle dg[032,035-036]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
-extended-96core-shared    up 3-12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-extended-96core-shared    up 3-12:00:00      3   idle dg[032,035-036]
-hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
-hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
-hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      3   plnd dn[050,061-062]
-large-40core              up    8:00:00      6 alloc@ dn[009,026,029,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      4    mix dn[004-005,018,051]
-large-40core              up    8:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-large-96core              up    8:00:00      2    mix dg[009,023]
-large-96core              up    8:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-large-96core              up    8:00:00      3   idle dg[032,035-036]
-long-40core               up 2-00:00:00      3   plnd dn[050,061-062]
-long-40core               up 2-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      4    mix dn[004-005,018,051]
-long-40core               up 2-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-long-40core-shared        up 1-00:00:00      3   plnd dn[050,061-062]
-long-40core-shared        up 1-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      4    mix dn[004-005,018,051]
-long-40core-shared        up 1-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core               up 2-00:00:00      2    mix dg[009,023]
-long-96core               up 2-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-long-96core               up 2-00:00:00      3   idle dg[032,035-036]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
-long-96core-shared        up 1-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-long-96core-shared        up 1-00:00:00      3   idle dg[032,035-036]
-medium-40core             up   12:00:00      3   plnd dn[050,061-062]
-medium-40core             up   12:00:00      6 alloc@ dn[009,026,029,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      4    mix dn[004-005,018,051]
-medium-40core             up   12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-medium-96core             up   12:00:00      2    mix dg[009,023]
-medium-96core             up   12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-medium-96core             up   12:00:00      3   idle dg[032,035-036]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      3   plnd dn[050,061-062]
-short-40core              up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      4    mix dn[004-005,018,051]
-short-40core              up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-short-40core-shared       up    4:00:00      3   plnd dn[050,061-062]
-short-40core-shared       up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      4    mix dn[004-005,018,051]
-short-40core-shared       up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core              up    4:00:00      2    mix dg[009,023]
-short-96core              up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-short-96core              up    4:00:00      3   idle dg[032,035-036]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core-shared       up    4:00:00      2    mix dg[009,023]
-short-96core-shared       up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
-short-96core-shared       up    4:00:00      3   idle dg[032,035-036]
-(base) [ehspector@milan2 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_vs_ ehspecto PD       0:00      6 (PartitionConfig)
-(base) [ehspector@milan2 ~]$ scancel 927435
-(base) [ehspector@milan2 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh
-Submitted batch job 928050
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Resources)
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto PD       0:00      6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtual_screen]$ scancel 928050
-(base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh
-Submitted batch job 928053
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       0:03      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       0:07      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       0:10      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       0:49      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtual_screen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       0:50      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtual_screen]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       1:42      3 dg[032,035-036]
-(base) [ehspector@milan2 Tutorials]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       1:43      3 dg[032,035-036]
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/
-(base) [ehspector@milan2 006_footprint]$ ls
-w26_footprint_scored.txt      2w26_hbond_scored.txt  footprint.in
-w26_footprint_scored.txt.pdf  2w26_scored.mol2       foot.sh
-(base) [ehspector@milan2 006_footprint]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       6:28      3 dg[032,035-036]
-(base) [ehspector@milan2 006_footprint]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       6:29      3 dg[032,035-036]
-(base) [ehspector@milan2 006_footprint]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       6:56      3 dg[032,035-036]
-(base) [ehspector@milan2 006_footprint]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R       7:42      3 dg[032,035-036]
-(base) [ehspector@milan2 006_footprint]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ../5EEN/
-(base) [ehspector@milan2 5EEN]$ ls
-_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
-(base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
-(base) [ehspector@milan2 007_virtualscreen]$ ls
-virtual.in  virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      2    mix a100-[03,05]
-a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      2    mix a100-[03,05]
-a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      2    mix a100-[03,05]
-a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
-debug-40core              up    1:00:00      3   plnd dn[050,061-062]
-debug-40core              up    1:00:00      6 alloc@ dn[009,026,029,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      4    mix dn[004-005,018,051]
-debug-40core              up    1:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-extended-40core           up 7-00:00:00      3   plnd dn[050,061-062]
-extended-40core           up 7-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      4    mix dn[004-005,018,051]
-extended-40core           up 7-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-extended-40core-shared    up 3-12:00:00      3   plnd dn[050,061-062]
-extended-40core-shared    up 3-12:00:00      6 alloc@ dn[009,026,029,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      4    mix dn[004-005,018,051]
-extended-40core-shared    up 3-12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-extended-96core           up 7-00:00:00      1   plnd dg039
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core           up 7-00:00:00      2    mix dg[009,023]
-extended-96core           up 7-00:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-extended-96core-shared    up 3-12:00:00      1   plnd dg039
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
-extended-96core-shared    up 3-12:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
-hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
-hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      3   plnd dn[050,061-062]
-large-40core              up    8:00:00      6 alloc@ dn[009,026,029,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      4    mix dn[004-005,018,051]
-large-40core              up    8:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-large-96core              up    8:00:00      1   plnd dg039
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-large-96core              up    8:00:00      2    mix dg[009,023]
-large-96core              up    8:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-long-40core               up 2-00:00:00      3   plnd dn[050,061-062]
-long-40core               up 2-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      4    mix dn[004-005,018,051]
-long-40core               up 2-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-long-40core-shared        up 1-00:00:00      3   plnd dn[050,061-062]
-long-40core-shared        up 1-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      4    mix dn[004-005,018,051]
-long-40core-shared        up 1-00:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-long-96core               up 2-00:00:00      1   plnd dg039
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core               up 2-00:00:00      2    mix dg[009,023]
-long-96core               up 2-00:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-long-96core-shared        up 1-00:00:00      1   plnd dg039
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
-long-96core-shared        up 1-00:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-medium-40core             up   12:00:00      3   plnd dn[050,061-062]
-medium-40core             up   12:00:00      6 alloc@ dn[009,026,029,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      4    mix dn[004-005,018,051]
-medium-40core             up   12:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-medium-96core             up   12:00:00      1   plnd dg039
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-medium-96core             up   12:00:00      2    mix dg[009,023]
-medium-96core             up   12:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      3   plnd dn[050,061-062]
-short-40core              up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      4    mix dn[004-005,018,051]
-short-40core              up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-short-40core-shared       up    4:00:00      3   plnd dn[050,061-062]
-short-40core-shared       up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      4    mix dn[004-005,018,051]
-short-40core-shared       up    4:00:00     47  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
-short-96core              up    4:00:00      1   plnd dg039
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core              up    4:00:00      2    mix dg[009,023]
-short-96core              up    4:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-short-96core-shared       up    4:00:00      1   plnd dg039
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core-shared       up    4:00:00      2    mix dg[009,023]
-short-96core-shared       up    4:00:00     36  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.in
-(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928057
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      12:28      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      12:41      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      12:46      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      12:47      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      12:49      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      14:35      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      14:38      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      14:40      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      14:42      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ ls
-virtual.in  virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      15:00      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 2w26_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      15:06      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ scancel 928057
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_vs_ ehspecto  R      16:00      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      2    mix a100-[03,05]
-a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      2    mix a100-[03,05]
-a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      2    mix a100-[03,05]
-a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
-debug-40core              up    1:00:00      2   plnd dn[061-062]
-debug-40core              up    1:00:00      6 alloc@ dn[009,026,029,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      4    mix dn[004-005,018,051]
-debug-40core              up    1:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-extended-40core           up 7-00:00:00      2   plnd dn[061-062]
-extended-40core           up 7-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      4    mix dn[004-005,018,051]
-extended-40core           up 7-00:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-extended-40core-shared    up 3-12:00:00      2   plnd dn[061-062]
-extended-40core-shared    up 3-12:00:00      6 alloc@ dn[009,026,029,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      4    mix dn[004-005,018,051]
-extended-40core-shared    up 3-12:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-extended-96core           up 7-00:00:00      3   plnd dg[006,026,039]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core           up 7-00:00:00      2    mix dg[009,023]
-extended-96core           up 7-00:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-extended-96core-shared    up 3-12:00:00      3   plnd dg[006,026,039]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
-extended-96core-shared    up 3-12:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
-hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
-hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     79  alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      2   plnd dn[061-062]
-large-40core              up    8:00:00      6 alloc@ dn[009,026,029,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      4    mix dn[004-005,018,051]
-large-40core              up    8:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-large-96core              up    8:00:00      3   plnd dg[006,026,039]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-large-96core              up    8:00:00      2    mix dg[009,023]
-large-96core              up    8:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-long-40core               up 2-00:00:00      2   plnd dn[061-062]
-long-40core               up 2-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      4    mix dn[004-005,018,051]
-long-40core               up 2-00:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-long-40core-shared        up 1-00:00:00      2   plnd dn[061-062]
-long-40core-shared        up 1-00:00:00      6 alloc@ dn[009,026,029,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      4    mix dn[004-005,018,051]
-long-40core-shared        up 1-00:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-long-96core               up 2-00:00:00      3   plnd dg[006,026,039]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core               up 2-00:00:00      2    mix dg[009,023]
-long-96core               up 2-00:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-long-96core-shared        up 1-00:00:00      3   plnd dg[006,026,039]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
-long-96core-shared        up 1-00:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-medium-40core             up   12:00:00      2   plnd dn[061-062]
-medium-40core             up   12:00:00      6 alloc@ dn[009,026,029,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      4    mix dn[004-005,018,051]
-medium-40core             up   12:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-medium-96core             up   12:00:00      3   plnd dg[006,026,039]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-medium-96core             up   12:00:00      2    mix dg[009,023]
-medium-96core             up   12:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      2   plnd dn[061-062]
-short-40core              up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      4    mix dn[004-005,018,051]
-short-40core              up    4:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-short-40core-shared       up    4:00:00      2   plnd dn[061-062]
-short-40core-shared       up    4:00:00      6 alloc@ dn[009,026,029,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      4    mix dn[004-005,018,051]
-short-40core-shared       up    4:00:00     48  alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
-short-96core              up    4:00:00      3   plnd dg[006,026,039]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core              up    4:00:00      2    mix dg[009,023]
-short-96core              up    4:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-short-96core-shared       up    4:00:00      3   plnd dg[006,026,039]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core-shared       up    4:00:00      2    mix dg[009,023]
-short-96core-shared       up    4:00:00     34  alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
-(base) [ehspector@milan2 007_virtualscreen]$ cd ../
-(base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928060
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
-short-96c 2w26_vs_ ehspecto  R      19:15      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
-short-96c 2w26_vs_ ehspecto  R      19:17      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
-short-96c 2w26_vs_ ehspecto  R      19:18      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
-short-96c 2w26_vs_ ehspecto  R      19:19      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      19:38      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      19:40      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      19:41      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928063
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Priority)
-short-96c 2w26_vs_ ehspecto  R      21:35      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ scancel 928063
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      21:54      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
-sbatch: error: QOSMaxNodePerJobLimit
-sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928066
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:11      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:13      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:13      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:16      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:17      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:17      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      23:18      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      24:32      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      24:38      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      24:39      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928070
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      25:10      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 2w26_vs_ ehspecto  R      25:19      3 dg[032,035-036]
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-(base) [ehspector@milan2 007_virtualscreen]$ scancel 928066
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      25:37      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      25:50      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto PD       0:00      3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 2w26_vs_ ehspecto  R      25:51      3 dg[032,035-036]
-(base) [ehspector@milan2 007_virtualscreen]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@login.seawulf.stonybrook.edu
-ehspector@login.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-****IMPORTANT MESSAGE BELOW****
-In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
-(base) [ehspector@login2 ~]$ cd ..
-(base) [ehspector@login2 home]$ home
-(base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ../../install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-amake[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock\
-> ^C
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Thu Feb 13 11:05:05 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:778:5: error: ‘Filter’ was not declared in this scope
-|     Filter filter;
-      |     ^12:36, 21 February 2025 (EST)
-make[1]: *** [dockmol.o] Error 1
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [dock] Error 2
-(base) [ehspector@login2 install]$ cd ../../
-(base) [ehspector@login2 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ../../
-(base) [ehspector@login2 alpha_branch]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-(base) [ehspector@login2 alpha_branch]$ cd install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Thu Feb 13 11:07:50 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
-g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
-g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
-g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
-g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
-g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
-g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
-g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
-g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
-g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
-g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
-g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
-g++ -c -O2 -std=c++11 -o score.o  score.cpp
-g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
-g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
-g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
-g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
-g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
-g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
-g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
-g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
-g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
-g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
-g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
-g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
-g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
-g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
-g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
-g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
-g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
-cd nab && make all
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-lm -lpthread
-mv dock6 ../../bin
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-(base) [ehspector@login2 install]$ cd ../
-(base) [ehspector@login2 alpha_branch]$ cd ../
-(base) [ehspector@login2 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ..
-(base) [ehspector@login2 src]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Thu Feb 13 11:20:49 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘gasteiger’; did you mean ‘gasteigerize’?
-|     if (filter.gasteiger){
-      |                ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-      |                gasteigerize
-dockmol.cpp:931:5: error: jump to label ‘skip’
-|     skip:
-      |     ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp:918:10: note:   from here
-|     goto skip;
-      |          ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp:919:9: note:   crosses initialization of ‘int num_zeros’
-|     int num_zeros = 0;
-      |         ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-make[1]: *** [dockmol.o] Error 1
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [dock] Error 2
-(base) [ehspector@login2 install]$ cd ..
-(base) [ehspector@login2 alpha_branch]$ cd src/dock
-(base) [ehspector@login2 dock]$ vi dockmol.cpp
-(base) [ehspector@login2 dock]$ cd ..
-\(base) [ehspector@login2 src]$ cd ../
-(base) [ehspector@login2 alpha_branch]$ cd install/
-(base) [ehspector@login2 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@login2 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Thu Feb 13 11:25:35 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -o amber_typer.o  amber_typer.cpp
-g++ -c -O2 -std=c++11 -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -o base_mpi.o  base_mpi.cpp
-g++ -c -O2 -std=c++11 -o base_score.o  base_score.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ag.o  conf_gen_ag.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_cg.o  conf_gen_cg.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn.o  conf_gen_dn.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_ga.o  conf_gen_ga.cpp
-g++ -c -O2 -std=c++11 -o conf_gen_hdb.o  conf_gen_hdb.cpp
-g++ -c -O2 -std=c++11 -o dock.o  dock.cpp
-g++ -c -O2 -std=c++11 -o dockmol.o  dockmol.cpp
-g++ -c -O2 -std=c++11 -o filter.o  filter.cpp
-g++ -c -O2 -std=c++11 -o fingerprint.o  fingerprint.cpp
-g++ -c -O2 -std=c++11 -o fraggraph.o  fraggraph.cpp
-g++ -c -O2 -std=c++11 -o fragment.o  fragment.cpp
-g++ -c -O2 -std=c++11 -o gasteiger.o  gasteiger.cpp
-g++ -c -O2 -std=c++11 -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -o hungarian.o  hungarian.cpp
-g++ -c -O2 -std=c++11 -o library_file.o  library_file.cpp
-g++ -c -O2 -std=c++11 -o limit_max_change.o  limit_max_change.cpp
-g++ -c -O2 -std=c++11 -o master_conf.o  master_conf.cpp
-g++ -c -O2 -std=c++11 -o master_score.o  master_score.cpp
-g++ -c -O2 -std=c++11 -o orient.o  orient.cpp
-g++ -c -O2 -std=c++11 -o sasa.o  sasa.cpp
-g++ -c -O2 -std=c++11 -o score.o  score.cpp
-g++ -c -O2 -std=c++11 -o score_amber.o  score_amber.cpp
-g++ -c -O2 -std=c++11 -o score_chemgrid.o  score_chemgrid.cpp
-g++ -c -O2 -std=c++11 -o score_descriptor.o  score_descriptor.cpp
-g++ -c -O2 -std=c++11 -o score_footprint.o  score_footprint.cpp
-g++ -c -O2 -std=c++11 -o score_ph4.o  score_ph4.cpp
-g++ -c -O2 -std=c++11 -o score_volume.o  score_volume.cpp
-g++ -c -O2 -std=c++11 -o score_gist.o  score_gist.cpp
-g++ -c -O2 -std=c++11 -o score_hbond.o  score_hbond.cpp
-g++ -c -O2 -std=c++11 -o score_internal.o  score_internal.cpp
-g++ -c -O2 -std=c++11 -o score_multigrid.o  score_multigrid.cpp
-g++ -c -O2 -std=c++11 -o score_sasa.o  score_sasa.cpp
-g++ -c -O2 -std=c++11 -o score_solvent.o  score_solvent.cpp
-g++ -c -O2 -std=c++11 -o simplex.o  simplex.cpp
-g++ -c -O2 -std=c++11 -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -o utils.o  utils.cpp
-g++ -c -O2 -std=c++11 -o iso_align.o  iso_align.cpp
-g++ -c -O2 -std=c++11 -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -o rdtyper.o  rdtyper.cpp
-g++ -c -O2 -std=c++11 -o rddrive.o  rddrive.cpp
-cd nab && make all
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-lm -lpthread
-mv dock6 ../../bin
-make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Thu Feb 13 11:27:30 EST 2025.
-(base) [ehspector@login2 install]$ cd
-(base) [ehspector@login2 ~]$ home
-(base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2          gas_3.out              gas_5.out              no_gas.in
-AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out_scored.mol2  no_gas.out
-gas_2.in               gas_4.in               gas.in                 no_gas.out_scored.mol2
-gas_2.out              gas_4.out              gas.out                test.mol2
-gas_2.out_scored.mol2  gas_4.out_scored.mol2  gas.out_scored.mol2    test_nocharge.mol2
-gas_3.in               gas_5.in               no_charge
-(base) [ehspector@login2 gas_teiger]$ mkdir test
-(base) [ehspector@login2 gas_teiger]$ vi gas_3.in
-(base) [ehspector@login2 gas_teiger]$ mv test_nocharge.mol2 test
-(base) [ehspector@login2 gas_teiger]$ mv gas_3.in
-mv: missing destination file operand after ‘gas_3.in’
-Try 'mv --help' for more information.
-(base) [ehspector@login2 gas_teiger]$ mv gas_3.in test
-(base) [ehspector@login2 gas_teiger]$ cd test/
-(base) [ehspector@login2 test]$ ls
-gas_3.in  test_nocharge.mol2
-(base) [ehspector@login2 test]$ vi test_nocharge.mol2
-(base) [ehspector@login2 test]$ vi gas_3.in
-(base) [ehspector@login2 test]$ dock6 -i gas_3.in -o gas_3.out
-(base) [ehspector@login2 test]$ ls
-gas_3.in  gas_3.out  gas_3.out_scored.mol2  test_nocharge.mol2
-(base) [ehspector@login2 test]$ vi gas_3.out
-(base) [ehspector@login2 test]$ vi gas_3.out_scored.mol2
-(base) [ehspector@login2 test]$ vi gas_3.out
-(base) [ehspector@login2 test]$ cd ..
-(base) [ehspector@login2 gas_teiger]$ cd ..
-(base) [ehspector@login2 4s0v]$ cd gas_teiger/
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2          gas_3.out              gas_5.in               gas.out_scored.mol2     test
-AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out              no_charge               test.mol2
-gas_2.in               gas_4.in               gas_5.out_scored.mol2  no_gas.in
-gas_2.out              gas_4.out              gas.in                 no_gas.out
-gas_2.out_scored.mol2  gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.in
-(base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@login2 gas_teiger]$ ls
-AAQ_noG.mol2          gas_3.out              gas_5.in               gas.out_scored.mol2     test
-AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out              no_charge               test.mol2
-gas_2.in               gas_4.in               gas_5.out_scored.mol2  no_gas.in
-gas_2.out              gas_4.out              gas.in                 no_gas.out
-gas_2.out_scored.mol2  gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2
-(base) [ehspector@login2 gas_teiger]$ cd ..
-(base) [ehspector@login2 4s0v]$ cd gas_teiger/
-(base) [ehspector@login2 gas_teiger]$ mv gas_4.in test
-(base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2
-mv: missing destination file operand after ‘1AAQ_noG.mol2’
-Try 'mv --help' for more information.
-(base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2 test
-(base) [ehspector@login2 gas_teiger]$ home
-(base) [ehspector@login2 espector]$ rd
-srun: error: invalid partition specified: short-40core
-srun: error: Unable to allocate resources: Invalid partition name specified
-(base) [ehspector@login2 espector]$ exit
-logout
-Connection to login.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ rd
-srun: job 928167 queued and waiting for resources
-^Csrun: Job allocation 928167 has been revoked
-srun: Force Terminated job 928167
-(base) [ehspector@milan1 ~]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       0:23      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:11:38      3 dg[032,035-036]
-(base) [ehspector@milan1 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       0:30      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:11:45      3 dg[032,035-036]
-(base) [ehspector@milan1 ~]$ cd ..
-(base) [ehspector@milan1 home]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/1O86/007_virtualscreen/
-(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtualscreen]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      1   mix@ a100-02
-a100                      up    8:00:00      2 alloc@ a100-[07,09]
-a100                      up    8:00:00      1 drain* a100-01
-a100                      up    8:00:00      2    mix a100-[03,05]
-a100                      up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-large                up    8:00:00      1   mix@ a100-02
-a100-large                up    8:00:00      2 alloc@ a100-[07,09]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      2    mix a100-[03,05]
-a100-large                up    8:00:00      5  alloc a100-[04,06,08,10-11]
-a100-long                 up 2-00:00:00      1   mix@ a100-02
-a100-long                 up 2-00:00:00      2 alloc@ a100-[07,09]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      2    mix a100-[03,05]
-a100-long                 up 2-00:00:00      5  alloc a100-[04,06,08,10-11]
-debug-40core              up    1:00:00      6   plnd dn[024-025,054,056-058]
-debug-40core              up    1:00:00      5 alloc@ dn[026,029,035,038,045]
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      5    mix dn[004-005,018,051,061]
-debug-40core              up    1:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-extended-40core           up 7-00:00:00      6   plnd dn[024-025,054,056-058]
-extended-40core           up 7-00:00:00      5 alloc@ dn[026,029,035,038,045]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      5    mix dn[004-005,018,051,061]
-extended-40core           up 7-00:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-extended-40core-shared    up 3-12:00:00      6   plnd dn[024-025,054,056-058]
-extended-40core-shared    up 3-12:00:00      5 alloc@ dn[026,029,035,038,045]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      5    mix dn[004-005,018,051,061]
-extended-40core-shared    up 3-12:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-extended-96core           up 7-00:00:00      1   mix@ dg040
-extended-96core           up 7-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core           up 7-00:00:00      2    mix dg[009,023]
-extended-96core           up 7-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-extended-96core           up 7-00:00:00      3   idle dg[042,046-047]
-extended-96core-shared    up 3-12:00:00      1   mix@ dg040
-extended-96core-shared    up 3-12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-extended-96core-shared    up 3-12:00:00      2    mix dg[009,023]
-extended-96core-shared    up 3-12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-extended-96core-shared    up 3-12:00:00      3   idle dg[042,046-047]
-hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[045-047]
-hbm-1tb-long-96core       up 2-00:00:00      1   idle xm048
-hbm-extended-96core       up 7-00:00:00      3   plnd xm[003,006-007]
-hbm-extended-96core       up 7-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-extended-96core       up 7-00:00:00      1  drain xm017
-hbm-extended-96core       up 7-00:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-large-96core          up    8:00:00      3   plnd xm[003,006-007]
-hbm-large-96core          up    8:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-large-96core          up    8:00:00      1  drain xm017
-hbm-large-96core          up    8:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-long-96core           up 2-00:00:00      3   plnd xm[003,006-007]
-hbm-long-96core           up 2-00:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-long-96core           up 2-00:00:00      1  drain xm017
-hbm-long-96core           up 2-00:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-medium-96core         up   12:00:00      3   plnd xm[003,006-007]
-hbm-medium-96core         up   12:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-medium-96core         up   12:00:00      1  drain xm017
-hbm-medium-96core         up   12:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
-hbm-short-96core          up    4:00:00      3   plnd xm[003,006-007]
-hbm-short-96core          up    4:00:00     10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
-hbm-short-96core          up    4:00:00      1  drain xm017
-hbm-short-96core          up    4:00:00     76  alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
-large-40core              up    8:00:00      6   plnd dn[024-025,054,056-058]
-large-40core              up    8:00:00      5 alloc@ dn[026,029,035,038,045]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      5    mix dn[004-005,018,051,061]
-large-40core              up    8:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-large-96core              up    8:00:00      1   mix@ dg040
-large-96core              up    8:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-large-96core              up    8:00:00      2    mix dg[009,023]
-large-96core              up    8:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-large-96core              up    8:00:00      3   idle dg[042,046-047]
-long-40core               up 2-00:00:00      6   plnd dn[024-025,054,056-058]
-long-40core               up 2-00:00:00      5 alloc@ dn[026,029,035,038,045]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      5    mix dn[004-005,018,051,061]
-long-40core               up 2-00:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-long-40core-shared        up 1-00:00:00      6   plnd dn[024-025,054,056-058]
-long-40core-shared        up 1-00:00:00      5 alloc@ dn[026,029,035,038,045]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      5    mix dn[004-005,018,051,061]
-long-40core-shared        up 1-00:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-long-96core               up 2-00:00:00      1   mix@ dg040
-long-96core               up 2-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core               up 2-00:00:00      2    mix dg[009,023]
-long-96core               up 2-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-long-96core               up 2-00:00:00      3   idle dg[042,046-047]
-long-96core-shared        up 1-00:00:00      1   mix@ dg040
-long-96core-shared        up 1-00:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-long-96core-shared        up 1-00:00:00      2    mix dg[009,023]
-long-96core-shared        up 1-00:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-long-96core-shared        up 1-00:00:00      3   idle dg[042,046-047]
-medium-40core             up   12:00:00      6   plnd dn[024-025,054,056-058]
-medium-40core             up   12:00:00      5 alloc@ dn[026,029,035,038,045]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      5    mix dn[004-005,018,051,061]
-medium-40core             up   12:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-medium-96core             up   12:00:00      1   mix@ dg040
-medium-96core             up   12:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-medium-96core             up   12:00:00      2    mix dg[009,023]
-medium-96core             up   12:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-medium-96core             up   12:00:00      3   idle dg[042,046-047]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      6   plnd dn[024-025,054,056-058]
-short-40core              up    4:00:00      5 alloc@ dn[026,029,035,038,045]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      5    mix dn[004-005,018,051,061]
-short-40core              up    4:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-short-40core-shared       up    4:00:00      6   plnd dn[024-025,054,056-058]
-short-40core-shared       up    4:00:00      5 alloc@ dn[026,029,035,038,045]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      5    mix dn[004-005,018,051,061]
-short-40core-shared       up    4:00:00     44  alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
-short-96core              up    4:00:00      1   mix@ dg040
-short-96core              up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core              up    4:00:00      2    mix dg[009,023]
-short-96core              up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-short-96core              up    4:00:00      3   idle dg[042,046-047]
-short-96core-shared       up    4:00:00      1   mix@ dg040
-short-96core-shared       up    4:00:00      7 alloc@ dg[013,024,028-029,033-034,043]
-short-96core-shared       up    4:00:00      2    mix dg[009,023]
-short-96core-shared       up    4:00:00     34  alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
-short-96core-shared       up    4:00:00      3   idle dg[042,046-047]
-(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.in
-(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928174
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       3:06      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:14:21      3 dg[032,035-036]
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       3:49      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:15:04      3 dg[032,035-036]
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       3:52      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:15:07      3 dg[032,035-036]
-(base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh
-Submitted batch job 928179
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 1O86_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 5een_vs_ ehspecto  R       4:21      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:15:36      3 dg[032,035-036]
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 1O86_vs_ ehspecto PD       0:00      3 (Priority)
-short-96c 5een_vs_ ehspecto  R       4:22      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:15:37      3 dg[032,035-036]
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       4:55      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:16:10      3 dg[032,035-036]
-short-96c 1O86_vs_ ehspecto  R       0:24      3 dg[026,046-047]
-(base) [ehspector@milan1 007_virtualscreen]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R       5:47      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:17:02      3 dg[032,035-036]
-short-96c 1O86_vs_ ehspecto  R       1:16      3 dg[026,046-047]
-(base) [ehspector@milan1 007_virtualscreen]$ home
-(base) [ehspector@milan1 espector]$ rd
-srun: job 928192 queued and waiting for resources
-srun: job 928192 has been allocated resources
-(base) [ehspector@dn050 espector]$ cd builds/alpha_branch/install/
-(base) [ehspector@dn050 install]$ ls
-bluegenel  docker    gnu.parallel        homebrew        intel.intelmpi.parallel  Makefile  sgi
-bluegenep  gnu       gnu.parallel.rdkit  homebrew.rdkit  intel.ip.mkl             oneapi    sgi.parallel
-config.h   gnu.acml  gnu.rdkit           ibmaix          intel.mkl                pgi       test
-configure  gnu.gdb   gnu.valgrind        intel           intel.parallel           rules.h
-(base) [ehspector@dn050 install]$ configure gnu.rdkit
-bash: configure: command not found
-(base) [ehspector@dn050 install]$ ./configure gnu.rdkit
-The requested configuration file was found.
-Warning: the configuration file already exists with the creation stamp:
-# Created at Wed Feb 12 10:29:31 EST 2025 via ./configure gnu
-It will be overwritten !
-Don't forget to make clean before rebuilding.
-To reconfigure and rebuild everything start with make -i distclean:
-Reconfiguring after make -i distclean will avoid this warning.
-The DOCK configuration file has been created.
- REQUIREMENTS - define these environment variables
- RDBASE is the root directory of RDKit
- BOOST is the root directory of Boost
-(base) [ehspector@dn050 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn050 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Thu Feb 13 11:55:37 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fingerprint.h:13,
-                 from fingerprint.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fingerprint.h:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fraggraph.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fraggraph.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fragment.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from gasteiger.h:8,
-                 from gasteiger.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from gasteiger.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from hungarian.h:7,
-                 from hungarian.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from hungarian.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from library_file.h:9,
-                 from library_file.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from library_file.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from limit_max_change.h:12,
-                 from limit_max_change.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from limit_max_change.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from master_conf.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from master_conf.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from master_score.cpp:2:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from master_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from orient.h:7,
-                 from orient.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from orient.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from sasa.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from sasa.h:14:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_amber.cpp:66:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_amber.cpp:55:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_chemgrid.cpp:39:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_chemgrid.cpp:38:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_descriptor.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_descriptor.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_footprint.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_footprint.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_ph4.h:7,
-                 from score_ph4.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_ph4.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_volume.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_volume.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_gist.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_gist.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_hbond.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_hbond.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_internal.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_internal.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_multigrid.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_multigrid.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_sasa.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_sasa.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_solvent.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_solvent.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from simplex.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from simplex.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from utils.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from utils.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.h:12,
-                 from iso_align.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fragment.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
-                 from rdtyper.cpp:18:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from rdtyper.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from rddrive.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from dockmol.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-cd nab && make all
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
-mv dock6.rdkit ../../bin
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
-DOCK v6.12
-program dock is complete at Thu Feb 13 11:58:47 EST 2025.
-(base) [ehspector@dn050 install]$ cd ..
-(base) [ehspector@dn050 alpha_branch]$ exit
-exit
-(base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/test/
-(base) [ehspector@milan1 test]$ ls
-AAQ_noG.mol2  gas_3.in  gas_3.out  gas_3.out_scored.mol2  gas_4.in  test_nocharge.mol2
-(base) [ehspector@milan1 test]$ vi gas_4.in
-(base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 test]$ ls
-AAQ_noG.mol2  gas_3.in  gas_3.out  gas_3.out_scored.mol2  gas_4.in  gas_4.out  test_nocharge.mol2
-(base) [ehspector@milan1 test]$ vi gas_4.out
-(base) [ehspector@milan1 test]$ vi gas_4.in
-(base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 test]$ ls
-AAQ_noG.mol2  gas_3.out              gas_4.in   gas_4.out_scored.mol2
-gas_3.in       gas_3.out_scored.mol2  gas_4.out  test_nocharge.mol2
-(base) [ehspector@milan1 test]$ vi gas_4.out
-(base) [ehspector@milan1 test]$ vi gas_4.in
-(base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan1 test]$ ls
-AAQ_noG.mol2  gas_3.out              gas_4.in   gas_4.out_scored.mol2
-gas_3.in       gas_3.out_scored.mol2  gas_4.out  test_nocharge.mol2
-(base) [ehspector@milan1 test]$ vi gas_4.out
-(base) [ehspector@milan1 test]$ vi gas_4.out_scored.mol2
-(base) [ehspector@milan1 test]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-40c 5een_vs_ ehspecto PD       0:00      4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
-short-96c 5een_vs_ ehspecto  R      16:05      3 dg[007-008,041]
-short-96c 2w26_vs_ ehspecto  R    1:27:20      3 dg[032,035-036]
-short-96c 1O86_vs_ ehspecto  R      11:34      3 dg[026,046-047]
-(base) [ehspector@milan1 test]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 1O86_vs_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-(base) [ehspector@milan2 ~]$ scancel 928174
-(base) [ehspector@milan2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan2 ~]$ cd AMS_536/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/007_virtual_screen/
-(base) [ehspector@milan2 007_virtual_screen]$ ls
-virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
-(base) [ehspector@milan2 007_virtual_screen]$ grep -c "Name" virtual_scored.mol2
-(base) [ehspector@milan2 007_virtual_screen]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 5EEN/007_virtualscreen/
-(base) [ehspector@milan2 007_virtualscreen]$ ls
-virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
-(base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2
-(base) [ehspector@milan2 007_virtualscreen]$ cd ../../1O86/007_virtualscreen/
-(base) [ehspector@milan2 007_virtualscreen]$ ls
-virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
-(base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2
-(base) [ehspector@milan2 007_virtualscreen]$ cd ../../
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/
-(base) [ehspector@milan2 006_footprint]$ pwd
-/gpfs/home/ehspector/AMS_536/Tutorials/2w26/006_footprint
-(base) [ehspector@milan2 006_footprint]$ cd ../
-(base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan2 007_virtual_screen]$ ls
-virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
-(base) [ehspector@milan2 007_virtual_screen]$ cd ../../5EEN/
-(base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
-(base) [ehspector@milan2 007_virtualscreen]$ cd ../
-(base) [ehspector@milan2 5EEN]$ cd ../
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ cd 007_virtualscreen/
-(base) [ehspector@milan2 007_virtualscreen]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan2 ~]$ cd AMS_536/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ home
-(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@milan2 dock]$ ls
-amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
-amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
-amber_typer.o       fingerprint.h         nab                   score_internal.o
-base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
-base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
-base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
-base_mpi.cpp        fraggraph.o           orient.h              score.o
-base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
-base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
-base_score.cpp      fragment.o            rddrive.h             score_ph4.o
-base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
-base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
-conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
-conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
-conf_gen_ag.o       grid.h                README                score_solvent.h
-conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
-conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
-conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
-conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
-conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
-conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
-conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
-conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
-conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
-conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
-conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
-conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
-conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
-conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
-conf_gen_hdb.o      lol                   score_footprint.h     trace.o
-defreal.h           Makefile              score_footprint.o     utils.cpp
-dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
-dockmol.cpp         master_conf.h         score_gist.h          utils.o
-dockmol.h           master_conf.o         score_gist.o          version.h
-dockmol.o           master_score.cpp      score.h               xlogp.cpp
-dock.o              master_score.h        score_hbond.cpp       xlogp.h
-filter.cpp          master_score.o        score_hbond.h
-filter.h            mem_info.cpp          score_hbond.o
-(base) [ehspector@milan2 dock]$ ls
-amber_typer.cpp     filter.o              mem_info.h            score_internal.cpp
-amber_typer.h       fingerprint.cpp       mem_info.o            score_internal.h
-amber_typer.o       fingerprint.h         nab                   score_internal.o
-base_grid.cpp       fingerprint.o         nabcode.h             score_multigrid.cpp
-base_grid.h         fraggraph.cpp         nab.h                 score_multigrid.h
-base_grid.o         fraggraph.h           orient.cpp            score_multigrid.o
-base_mpi.cpp        fraggraph.o           orient.h              score.o
-base_mpi.h          fragment.cpp          orient.o              score_ph4.cpp
-base_mpi.o          fragment.h            rddrive.cpp           score_ph4.h
-base_score.cpp      fragment.o            rddrive.h             score_ph4.o
-base_score.h        gasteiger.cpp         rddrive.o             score_sasa.cpp
-base_score.o        gasteiger.h           rdtyper.cpp           score_sasa.h
-conf_gen_ag.cpp     gasteiger.o           rdtyper.h             score_sasa.o
-conf_gen_ag.h       grid.cpp              rdtyper.o             score_solvent.cpp
-conf_gen_ag.o       grid.h                README                score_solvent.h
-conf_gen_cg.cpp     grid.o                sasa.cpp              score_solvent.o
-conf_gen_cg.h       gzstream              sasa.h                score_volume.cpp
-conf_gen_cg.o       hungarian.cpp         sasa.o                score_volume.h
-conf_gen_dn.cpp     hungarian.h           score_amber.cpp       score_volume.o
-conf_gen_dn_ga.cpp  hungarian.o           score_amber.h         simplex.cpp
-conf_gen_dn_ga.h    iso_align.cpp         score_amber.o         simplex.h
-conf_gen_dn_ga.o    iso_align.h           score_chemgrid.cpp    simplex.o
-conf_gen_dn.h       iso_align.o           score_chemgrid.h      sphere.cpp
-conf_gen_dn.o       library_file.cpp      score_chemgrid.o      sphere.h
-conf_gen_ga.cpp     library_file.h        score.cpp             sphere.o
-conf_gen_ga.h       library_file.o        score_descriptor.cpp  tnt
-conf_gen_ga.o       limit_max_change.cpp  score_descriptor.h    trace.cpp
-conf_gen_hdb.cpp    limit_max_change.h    score_descriptor.o    trace.h
-conf_gen_hdb.h      limit_max_change.o    score_footprint.cpp   trace.inl
-conf_gen_hdb.o      lol                   score_footprint.h     trace.o
-defreal.h           Makefile              score_footprint.o     utils.cpp
-dock.cpp            master_conf.cpp       score_gist.cpp        utils.h
-dockmol.cpp         master_conf.h         score_gist.h          utils.o
-dockmol.h           master_conf.o         score_gist.o          version.h
-dockmol.o           master_score.cpp      score.h               xlogp.cpp
-dock.o              master_score.h        score_hbond.cpp       xlogp.h
-filter.cpp          master_score.o        score_hbond.h
-filter.h            mem_info.cpp          score_hbond.o
-(base) [ehspector@milan2 dock]$ grep parameters
-^C
-(base) [ehspector@milan2 dock]$ grep -c "parameters"
-^C
-(base) [ehspector@milan2 dock]$ grep -c "parameters" library_file.cpp
-(base) [ehspector@milan2 dock]$ vi library_file.cpp
-(base) [ehspector@milan2 dock]$ vi filter.cpp
-(base) [ehspector@milan2 dock]$ vi filter.cpp
-(base) [ehspector@milan2 dock]$ vi dockmol.cpp
-(base) [ehspector@milan2 dock]$ rd
-srun: job 931653 queued and waiting for resources
-srun: job 931653 has been allocated resources
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:28:08 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘mol_status’
-|     if (filter.mol_status = false){
-      |                ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:30:26 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ ls
-alpha_branch  dock6-master  dock6-master.zip  dock6-rdkit
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/
-(base) [ehspector@dn033 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@dn033 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@dn033 src]$ cd dock
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:33:59 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = no){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-dockmol.cpp:917:42: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?
-|     if (filter.gasteigerize.mol_status = no){
-      |                                          ^~
-      |                                          boost::concepts::detail::no
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here
-|   typedef char (&no)[2];
-      |                  ^~
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ ls
-amber_typer.cpp     conf_gen_hdb.o        master_conf.cpp       score.h
-amber_typer.h       defreal.h             master_conf.h         score_hbond.cpp
-amber_typer.o       dock.cpp              master_score.cpp      score_hbond.h
-base_grid.cpp       dockmol.cpp           master_score.h        score_internal.cpp
-base_grid.h         dockmol.h             mem_info.cpp          score_internal.h
-base_grid.o         dock.o                mem_info.h            score_multigrid.cpp
-base_mpi.cpp        filter.cpp            nab                   score_multigrid.h
-base_mpi.h          filter.h              nabcode.h             score_ph4.cpp
-base_mpi.o          fingerprint.cpp       nab.h                 score_ph4.h
-base_score.cpp      fingerprint.h         orient.cpp            score_sasa.cpp
-base_score.h        fraggraph.cpp         orient.h              score_sasa.h
-base_score.o        fraggraph.h           rddrive.cpp           score_solvent.cpp
-conf_gen_ag.cpp     fragment.cpp          rddrive.h             score_solvent.h
-conf_gen_ag.h       fragment.h            rdtyper.cpp           score_volume.cpp
-conf_gen_ag.o       gasteiger.cpp         rdtyper.h             score_volume.h
-conf_gen_cg.cpp     gasteiger.h           README                simplex.cpp
-conf_gen_cg.h       grid.cpp              sasa.cpp              simplex.h
-conf_gen_cg.o       grid.h                sasa.h                sphere.cpp
-conf_gen_dn.cpp     gzstream              score_amber.cpp       sphere.h
-conf_gen_dn_ga.cpp  hungarian.cpp         score_amber.h         tnt
-conf_gen_dn_ga.h    hungarian.h           score_chemgrid.cpp    trace.cpp
-conf_gen_dn_ga.o    iso_align.cpp         score_chemgrid.h      trace.h
-conf_gen_dn.h       iso_align.h           score.cpp             trace.inl
-conf_gen_dn.o       library_file.cpp      score_descriptor.cpp  utils.cpp
-conf_gen_ga.cpp     library_file.h        score_descriptor.h    utils.h
-conf_gen_ga.h       limit_max_change.cpp  score_footprint.cpp   version.h
-conf_gen_ga.o       limit_max_change.h    score_footprint.h     xlogp.cpp
-conf_gen_hdb.cpp    lol                   score_gist.cpp        xlogp.h
-conf_gen_hdb.h      Makefile              score_gist.h
-(base) [ehspector@dn033 dock]$ vi filter.cpp
-(base) [ehspector@dn033 dock]$ vi filter.h
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../
-(base) [ehspector@dn033 alpha_branch]$ ls
-bin        docs     parameters  README.md  template_pipeline
-developer  install  README      src        tutorials
-(base) [ehspector@dn033 alpha_branch]$ cd src/
-(base) [ehspector@dn033 src]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:45:39 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd src/
-(base) [ehspector@dn033 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@dn033 src]$ cd dock
-(base) [ehspector@dn033 dock]$ vi filter.cpp
-(base) [ehspector@dn033 dock]$ cd ../
-(base) [ehspector@dn033 src]$ vi dockmol.cpp
-(base) [ehspector@dn033 src]$ cd dock
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:52:20 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ..
-(base) [ehspector@dn033 alpha_branch]$ cd src/dock
-(base) [ehspector@dn033 dock]$ vi filter.cpp
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ..
-(base) [ehspector@dn033 src]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ ls
-bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
-bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
-config.h   gnu.parallel        ibmaix                   Makefile        test
-configure  gnu.parallel.rdkit  intel                    oneapi
-docker     gnu.rdkit           intel.intelmpi.parallel  pgi
-gnu        gnu.valgrind        intel.ip.mkl             rules.h
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:55:45 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-dockmol.cpp:917:43: warning: multi-character character constant [-Wmultichar]
-|     if (filter.gasteigerize.mol_status == 'no'){
-      |                                           ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status == 'no'){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ..
-(base) [ehspector@dn033 alpha_branch]$ cd src/dock
-(base) [ehspector@dn033 dock]$ vi filter.cpp
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 16:58:13 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ vi library_file.cpp
-(base) [ehspector@dn033 dock]$ vi library_file.h
-(base) [ehspector@dn033 dock]$ vi filter.cpp
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 17:06:34 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:29: error: ‘mol_status’ was not declared in this scope
-|     if (filter.gasteigerize(mol_status) = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-dockmol.cpp:917:39: error: expression cannot be used as a function
-|     if (filter.gasteigerize(mol_status) = false){
-      |                                       ^
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ vi filter.cpp
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ vi filter.cpp
-(base) [ehspector@dn033 dock]$ vi filter.h
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ..
-(base) [ehspector@dn033 src]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 17:16:17 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:917:30: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (!filter.gasteigerize.mol_status){
-      |                              ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd src/dock
-(base) [ehspector@dn033 dock]$ vi library_file.cpp
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 17:59:26 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:780:5: error: ‘mol_status’ was not declared in this scope
-|     mol_status = false;
-      |     ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ vi dockmol.cpp
-(base) [ehspector@dn033 install]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd ../
-(base) [ehspector@dn033 builds]$ cd ../
-(base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ..
-(base) [ehspector@dn033 src]$ cd ../
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 18:02:33 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/
-(base) [ehspector@dn033 src]$ ;s
-bash: syntax error near unexpected token `;'
-(base) [ehspector@dn033 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@dn033 src]$ cd dock
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 18:06:37 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:919:16: error: ‘gasteigerize’ is not a class, namespace, or enumeration
-|     if (filter.gasteigerize::mol_status = no){
-      |                ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
-dockmol.cpp:919:43: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?
-|     if (filter.gasteigerize::mol_status = no){
-      |                                           ^~
-      |                                           boost::concepts::detail::no
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here
-|   typedef char (&no)[2];
-      |                  ^~
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ vi dockmol.cpp
-(base) [ehspector@dn033 install]$ cd ..
-(base) [ehspector@dn033 alpha_branch]$ cd install/
-(base) [ehspector@dn033 install]$ ls
-bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
-bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
-config.h   gnu.parallel        ibmaix                   Makefile        test
-configure  gnu.parallel.rdkit  intel                    oneapi
-docker     gnu.rdkit           intel.intelmpi.parallel  pgi
-gnu        gnu.valgrind        intel.ip.mkl             rules.h
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd ..
-(base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 18:11:54 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:919:16: error: ‘class Filter’ has no member named ‘mol_status’
-|     if (filter.mol_status = false){
-      |                ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ..
-(base) [ehspector@dn033 alpha_branch]$ cd ..
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/
-(base) [ehspector@dn033 src]$ ;s
-bash: syntax error near unexpected token `;'
-(base) [ehspector@dn033 src]$ ls
-accessories  dock       gbsa_grids  Makefile  rdkit  tleap
-antechamber  docktools  grid        mopac6    resp
-(base) [ehspector@dn033 src]$ cd dock
-(base) [ehspector@dn033 dock]$ ls
-amber_typer.cpp     conf_gen_hdb.o        master_conf.cpp       score.h
-amber_typer.h       defreal.h             master_conf.h         score_hbond.cpp
-amber_typer.o       dock.cpp              master_score.cpp      score_hbond.h
-base_grid.cpp       dockmol.cpp           master_score.h        score_internal.cpp
-base_grid.h         dockmol.h             mem_info.cpp          score_internal.h
-base_grid.o         dock.o                mem_info.h            score_multigrid.cpp
-base_mpi.cpp        filter.cpp            nab                   score_multigrid.h
-base_mpi.h          filter.h              nabcode.h             score_ph4.cpp
-base_mpi.o          fingerprint.cpp       nab.h                 score_ph4.h
-base_score.cpp      fingerprint.h         orient.cpp            score_sasa.cpp
-base_score.h        fraggraph.cpp         orient.h              score_sasa.h
-base_score.o        fraggraph.h           rddrive.cpp           score_solvent.cpp
-conf_gen_ag.cpp     fragment.cpp          rddrive.h             score_solvent.h
-conf_gen_ag.h       fragment.h            rdtyper.cpp           score_volume.cpp
-conf_gen_ag.o       gasteiger.cpp         rdtyper.h             score_volume.h
-conf_gen_cg.cpp     gasteiger.h           README                simplex.cpp
-conf_gen_cg.h       grid.cpp              sasa.cpp              simplex.h
-conf_gen_cg.o       grid.h                sasa.h                sphere.cpp
-conf_gen_dn.cpp     gzstream              score_amber.cpp       sphere.h
-conf_gen_dn_ga.cpp  hungarian.cpp         score_amber.h         tnt
-conf_gen_dn_ga.h    hungarian.h           score_chemgrid.cpp    trace.cpp
-conf_gen_dn_ga.o    iso_align.cpp         score_chemgrid.h      trace.h
-conf_gen_dn.h       iso_align.h           score.cpp             trace.inl
-conf_gen_dn.o       library_file.cpp      score_descriptor.cpp  utils.cpp
-conf_gen_ga.cpp     library_file.h        score_descriptor.h    utils.h
-conf_gen_ga.h       limit_max_change.cpp  score_footprint.cpp   version.h
-conf_gen_ga.o       limit_max_change.h    score_footprint.h     xlogp.cpp
-conf_gen_hdb.cpp    lol                   score_gist.cpp        xlogp.h
-conf_gen_hdb.h      Makefile              score_gist.h
-(base) [ehspector@dn033 dock]$ vi dockmol.cpp
-(base) [ehspector@dn033 dock]$ cd ../../install/
-(base) [ehspector@dn033 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Sun Feb 16 18:14:22 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-makIn file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
-dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
-|     if (filter.gasteigerize.mol_status = false){
-      |                             ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn033 install]$ cd ../../
-(base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn033 dock]$ vi filter.h
-(base) [ehspector@dn033 dock]$ exit
-exit
-(base) [ehspector@milan2 dock]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Permission denied, please try again.
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
-. Duo Push to XXX-XXX-9204
-Passcode or option (1-1): 1
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ home
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock
-(base) [ehspector@milan2 dock]$ vi filter.cpp
-(base) [ehspector@milan2 dock]$ vi filter.cpp
-(base) [ehspector@milan2 dock]$ vi dockmol.cpp
-(base) [ehspector@milan2 dock]$ rd
-srun: job 932106 queued and waiting for resources
-srun: job 932106 has been allocated resources
-(base) [ehspector@dn035 dock]$ cd ../../install/
-(base) [ehspector@dn035 install]$ ls
-bluegenel  gnu.acml            homebrew                 intel.mkl       sgi
-bluegenep  gnu.gdb             homebrew.rdkit           intel.parallel  sgi.parallel
-config.h   gnu.parallel        ibmaix                   Makefile        test
-configure  gnu.parallel.rdkit  intel                    oneapi
-docker     gnu.rdkit           intel.intelmpi.parallel  pgi
-gnu        gnu.valgrind        intel.ip.mkl             rules.h
-(base) [ehspector@dn035 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn035 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 17 10:08:08 EST 2025.
-make -C ../src/dock  install
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp:214:7: error: expected unqualified-id before ‘else’
-|     } else {
-      |       ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp:221:5: error: ‘message’ does not name a type
-|     message = get_descriptors(mol);
-      |     ^12:36, 21 February 2025 (EST)~
-filter.cpp:222:5: error: ‘cout’ does not name a type
-|     cout << message << endl;
-      |     ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp:223:1: error: expected declaration before ‘}’ token
-| }
-      | ^
-make[1]: *** [../../install/rules.h:36: filter.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn035 install]$ module load git
-(base) [ehspector@dn035 install]$ git diff
-diff --git a/docs/new_in_6.13.txt b/docs/new_in_6.13.txt
-index 7b10f318..fac269c6 100644
---- a/docs/new_in_6.13.txt
-+++ b/docs/new_in_6.13.txt
-@@ -29,6 +29,14 @@ Ligand Efficiency added for Descriptor Score
-     Users can now toggle ligand efficiency on/off when using grid_score in descriptor score.
-     Ligand efficiency can be used alongside with grid score and will be calculated as the grid score divided by the number of heavy atoms.
-+Gasterization of molecules in database filter
+=== Selecting a Dummy Atom ===
-+    Users can now apply gasteiger charges using the databasefilter question tree
-+    instead of having to gasterize molecules through the GA. This will be a useful
-+    tool in benchmarking dock as well as understanding the electrostatics of a
-+    protein environment.
-+    Disclaimer: gasterization can be used as long as the molecule is precharged
-+    and acts mainly as an interconversion function.
-+
- Miscellaneous
- Mutation Selection algorithmic changes for DOCK_GA
-@@ -36,6 +44,8 @@ Mutation Selection algorithmic changes for DOCK_GA
-     the GA will not select a mutation type and then select a fragment
-     incompatible with the selected mutation type.
-+If users use sphere files, DOCK6 will print out the number of spheres used.
-+
-:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
- BUG FIXES
-@@ -67,6 +77,8 @@ definitions added:
-  definition    N.am
-  ______________________________________________________________________
-+Pertaining to the RDKit compilation with DOCK6, previous versions of DOCK6 included
-+a broken Boost url for download. Hence, we have replaced it with a working url.
-:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-@@ -88,6 +100,8 @@ For DOCK_GA:
-     ga_constraint_lower_mol_wt          [0]
-     ga_constraint_lower_mol_wt          [0]
-     ga_constraint_mol_wt_std_dev        [35.0]
-+For Database Filter:
-+    dbfilter_gasteiger_charges          [no] (yes no)
-:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-@@ -111,6 +125,10 @@ KNOWN BUGS
-. In the flex.defn file, there is a flag minimize which is disabled.
-        (The flag has no impact on the calculation.) All torsions are
-        Minimized.
-+
-+    4. Gasterization can be used as long as the molecule is precharged
-+       and acts mainly as an interconversion function.Additionally,ions
-+       will give calculating difficulty.
-:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-diff --git a/src/dock/dockmol.cpp b/src/dock/dockmol.cpp
-index 34811840..2f964a80 100644
---- a/src/dock/dockmol.cpp
-+++ b/src/dock/dockmol.cpp
-@@ -35,7 +35,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- #include <iomanip>
- #include <string.h>
- #include "dockmol.h"
--
-+#include "filter.h"
- #ifdef BUILD_DOCK_WITH_RDKIT
- #include <fstream>
- // RDKit stuff
-@@ -539,14 +539,14 @@ Read_Mol2_retain(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvat
-             mol.subst_names[i] = subst_name;//mol.title
-         }
-     }
--    // If all partial charges are zero, it is a bad molecule
-+    //If all partial charges are zero, it is a bad molecule
-     int num_zeros = 0;
-     for (int i = 0; i < mol.num_atoms; ++i){
-         if (mol.charges[i] == 0.0){
-             num_zeros += 1;
-         }
-     }
--    // Is it a bad molecule?
-+    //Is it a bad molecule?
-     if (num_zeros == mol.num_atoms){
-         mol.bad_molecule = true;
-     }
--    // Is it a bad molecule?
-+    //Is it a bad molecule?
-     if (num_zeros == mol.num_atoms){
-         mol.bad_molecule = true;
-     } else {
-@@ -775,7 +775,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
-     bool            check_cols = false;
-     bool            seven_columns = false; // default @<TRIPOS>ATOM line has 9 columns. By GDRM
-     //int             bad_line{0}; // number of bad atom lines. By GDRM
--
-+    //declaring classes for gasteiger bypass EHS 2/16/25
-+    Filter filter;
-+    Filter  mol_status;
-     // init state vars
-     atom_line = false;
-@@ -913,6 +915,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
-         }
-     }
-     // If all partial charges are zero, it is a bad molecule
-+    // Skip over if gasterizing a molecule with no charges EHS 2/13/25
-+    if (filter.gasteigerize){
-+    goto skip;
-     int num_zeros = 0;
-     for (int i = 0; i < mol.num_atoms; ++i){
-         if (mol.charges[i] == 0.0){
-@@ -925,6 +930,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
-     } else {
-         mol.bad_molecule = false;
-     }
-+}
-+    skip:
-+       cout << "This Molecule has no charges and will be gasterized" << endl;
-     // skip down to the bond section
-     for (;;) {
-diff --git a/src/dock/filter.cpp b/src/dock/filter.cpp
-index b8469418..58f9c742 100644
---- a/src/dock/filter.cpp
-+++ b/src/dock/filter.cpp
-@@ -196,14 +196,14 @@ void Filter::calc_descriptors(DOCKMol & mol, AMBER_TYPER & c_typer)
-         }
-         // placing a gasteiger flag this will be similar to ga code
--        if ( gasteigerize ){
--            //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25
--            activate_mol(mol);
-+        if ( gasteigerize && mol.bad_molecule == false ){
-+            //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25
-+           activate_mol(mol);
-(base) [ehspector@dn035 install]$
-(base) [ehspector@dn035 install]$ exit
-exit
-(base) [ehspector@milan2 dock]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+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_protein_wH_wcH.mol2 file, then your 1O86_ligand_wH_wcH.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:
-. Duo Push to XXX-XXX-9204
+[[File:Ligand_In_1O86_DN.png|600px]]
-Passcode or option (1-1): 1
+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:
-Pushed a login request to your device...
+[[File:1O86_Zone.png|600px]]
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ home
-(base) [ehspector@milan2 espector]$ cd 4s0v/
-(base) [ehspector@milan2 4s0v]$ ls
-cartesian_minimization  fixed_anchor_docking  footprint   genericDenovo  surface_spheres
-Denovodata              flex_docking          fragLib     gridbox        virtual_screening
-deNovorefinement        flex_docking_mpi      GA          reScore
-dock6_v_dock6mpi        focusGrowth           GA_data     rigid_docking
-energy_min              focusReScore          gas_teiger  structure
-(base) [ehspector@milan2 4s0v]$ cd gas_teiger/
-(base) [ehspector@milan2 gas_teiger]$ ls
-AAQ_yesG.mol2         gas_3.out_scored.mol2  gas_5.out_scored.mol2  no_gas.in
-gas_2.in               gas_4.out              gas.in                 no_gas.out
-gas_2.out              gas_4.out_scored.mol2  gas.out                no_gas.out_scored.mol2
-gas_2.out_scored.mol2  gas_5.in               gas.out_scored.mol2    test
-gas_3.out              gas_5.out              no_charge              test.mol2
-(base) [ehspector@milan2 gas_teiger]$ cd test/
-(base) [ehspector@milan2 test]$ ls
-AAQ_noG.mol2  gas_3.out              gas_4.in   gas_4.out_scored.mol2
-gas_3.in       gas_3.out_scored.mol2  gas_4.out  test_nocharge.mol2
-(base) [ehspector@milan2 test]$ vi gas_4.out
-(base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2
-(base) [ehspector@milan2 test]$ dock6 -i gas_4.in -o gas_4.out
-(base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2
-(base) [ehspector@milan2 test]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+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:
-. Duo Push to XXX-XXX-9204
+[[File:highlight.png|600px]]
-Passcode or option (1-1): 1
+To modify this image even further:
+Go to Actions >> Atoms/Bonds >> Show
+Next, navigate to Select >> Invert(selected models), here you'll notice most of the protein is highlighted
+Lastly, Return to Actions >> Atoms/Bonds >> delete
+You now see that there is a clearer picture of specifically, which atoms are interacting closely with the protein
-Pushed a login request to your device...
+[[File:Clear_picture.png|600px]]
-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
+You'll notice that there are two oxygens interacting with neighboring residues in the protein. Tracing your cursor
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
+in between the oxygens, you'll highlight a Carbon atom labeled C9. This will be the atom of choice for this tutorial.
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp:214:7: error: expected unqualified-id before ‘else’
-|     } else {
-      |       ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp:221:5: error: ‘message’ does not name a type
-|     message = get_descriptors(mol);
-      |     ^12:36, 21 February 2025 (EST)~
-filter.cpp:222:5: error: ‘cout’ does not name a type
-|     cout << message << endl;
-      |     ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp:223:1: error: expected declaration before ‘}’ token
-| }
-      | ^
-make[1]: *** [../../install/rules.h:36: filter.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn051 install]$ cd ../../
-(base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn051 dock]$ vi filter.cpp
-(base) [ehspector@dn051 dock]$ cd ../../install/
-(base) [ehspector@dn051 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn051 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 17 13:00:19 EST 2025.
-make -C ../src/dock  install
+=== Generating a Dummy Atom ===
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-filter.cpp: In member function ‘void Filter::calc_descriptors(DOCKMol&, AMBER_TYPER&)’:
-filter.cpp:279:26: error: qualified-id in declaration before ‘(’ token
-| bool Filter::fails_filter(DOCKMol & mol)
-      |                          ^
-filter.cpp:529:31: error: qualified-id in declaration before ‘(’ token
-| string Filter::get_descriptors(DOCKMol & mol)
-      |                               ^
-filter.cpp:591:21: error: qualified-id in declaration before ‘(’ token
-| Filter::activate_mol( DOCKMol & mol )
-      |                     ^
-filter.cpp:605:2: error: expected ‘}’ at end of input
-| } // end Filter::activate_mol()
-      |  ^
-filter.cpp:147:1: note: to match this ‘{’
-| {
-      | ^
-make[1]: *** [../../install/rules.h:36: filter.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn051 install]$ cd ../../alpha_branch/src/dock
-(base) [ehspector@dn051 dock]$ vi filter.cpp
-(base) [ehspector@dn051 dock]$ vi filter.cpp
-(base) [ehspector@dn051 dock]$ cd ../../install/
-(base) [ehspector@dn051 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn051 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 17 13:05:08 EST 2025.
-make -C ../src/dock  install
+Now that we have our atom of choice, we need to modify the ligand as well as the mol2 file itself.
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fingerprint.h:13,
-                 from fingerprint.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fingerprint.h:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fraggraph.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fraggraph.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fragment.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from gasteiger.h:8,
-                 from gasteiger.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from gasteiger.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from hungarian.h:7,
-                 from hungarian.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from hungarian.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from library_file.h:9,
-                 from library_file.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from library_file.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from limit_max_change.h:12,
-                 from limit_max_change.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from limit_max_change.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from master_conf.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from master_conf.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from master_score.cpp:2:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from master_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from orient.h:7,
-                 from orient.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from orient.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from sasa.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from sasa.h:14:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_amber.cpp:66:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_amber.cpp:55:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_chemgrid.cpp:39:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_chemgrid.cpp:38:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_descriptor.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_descriptor.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_footprint.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_footprint.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_ph4.h:7,
-                 from score_ph4.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_ph4.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_volume.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_volume.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_gist.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_gist.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_hbond.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_hbond.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_internal.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_internal.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_multigrid.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_multigrid.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_sasa.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_sasa.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_solvent.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_solvent.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from simplex.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from simplex.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from utils.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from utils.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.h:12,
-                 from iso_align.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fragment.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
-                 from rdtyper.cpp:18:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from rdtyper.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from rddrive.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from dockmol.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-cd nab && make all
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
-mv dock6.rdkit ../../bin
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-Installation of
+First, open the <code>1O86_ligand_wH_wcH.mol2</code> in Chimera.
-DOCK v6.12
-program dock is complete at Mon Feb 17 13:08:09 EST 2025.
-(base) [ehspector@dn051 install]$ cd ../al
+Locate the C9 atom >> select the two oxygens attached to C9 >> Atoms/Bonds >> delete.
-bash: cd: ../al: No such file or directory
+Then, save the mol2 file, lets call it 1O86_ligand_Du.mol2.
-(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
+Finally, we must open the mol2 file on our terminal or a text editor and change the atom type of C9 to Du:
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dock.cpp: In function ‘int main(int, char**)’:
-dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
-|     while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
-      |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-In file included from dock.cpp:62:
-library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
-|     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
-      |                     ^12:36, 21 February 2025 (EST)~
-library_file.h:141:21: note:   candidate expects 7 arguments, 8 provided
-make[1]: *** [../../install/rules.h:36: dock.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn051 install]$ cd ../
-(base) [ehspector@dn051 alpha_branch]$ cd ../
-(base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn051 dock]$ vi dock.cpp
-(base) [ehspector@dn051 dock]$ vi library_file.cpp
-(base) [ehspector@dn051 dock]$ vi dockmol.cpp
-(base) [ehspector@dn051 dock]$ ls
-amber_typer.cpp     conf_gen_dn.o     gzstream              rddrive.h             score_multigrid.h
-amber_typer.h       conf_gen_ga.cpp   hungarian.cpp         rdtyper.cpp           score_ph4.cpp
-amber_typer.o       conf_gen_ga.h     hungarian.h           rdtyper.h             score_ph4.h
-base_grid.cpp       conf_gen_ga.o     iso_align.cpp         README                score_sasa.cpp
-base_grid.h         conf_gen_hdb.cpp  iso_align.h           sasa.cpp              score_sasa.h
-base_grid.o         conf_gen_hdb.h    library_file.cpp      sasa.h                score_solvent.cpp
-base_mpi.cpp        conf_gen_hdb.o    library_file.h        score_amber.cpp       score_solvent.h
-base_mpi.h          defreal.h         limit_max_change.cpp  score_amber.h         score_volume.cpp
-base_mpi.o          dock.cpp          limit_max_change.h    score_chemgrid.cpp    score_volume.h
-base_score.cpp      dockmol.cpp       lol                   score_chemgrid.h      simplex.cpp
-base_score.h        dockmol.h         Makefile              score.cpp             simplex.h
-base_score.o        filter.cpp        master_conf.cpp       score_descriptor.cpp  sphere.cpp
-conf_gen_ag.cpp     filter.h          master_conf.h         score_descriptor.h    sphere.h
-conf_gen_ag.h       fingerprint.cpp   master_score.cpp      score_footprint.cpp   tnt
-conf_gen_ag.o       fingerprint.h     master_score.h        score_footprint.h     trace.cpp
-conf_gen_cg.cpp     fraggraph.cpp     mem_info.cpp          score_gist.cpp        trace.h
-conf_gen_cg.h       fraggraph.h       mem_info.h            score_gist.h          trace.inl
-conf_gen_cg.o       fragment.cpp      nab                   score.h               utils.cpp
-conf_gen_dn.cpp     fragment.h        nabcode.h             score_hbond.cpp       utils.h
-conf_gen_dn_ga.cpp  gasteiger.cpp     nab.h                 score_hbond.h         version.h
-conf_gen_dn_ga.h    gasteiger.h       orient.cpp            score_internal.cpp    xlogp.cpp
-conf_gen_dn_ga.o    grid.cpp          orient.h              score_internal.h      xlogp.h
-conf_gen_dn.h       grid.h            rddrive.cpp           score_multigrid.cpp
-(base) [ehspector@dn051 dock]$ vi dockmol.cpp
-(base) [ehspector@dn051 dock]$ vi dock.cpp
-(base) [ehspector@dn051 dock]$ vi library_file.cpp
-(base) [ehspector@dn051 dock]$ vi dock.cpp
-(base) [ehspector@dn051 dock]$ cd ../../
-(base) [ehspector@dn051 alpha_branch]$ cd install/
-(base) [ehspector@dn051 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn051 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 17 13:40:15 EST 2025.
-make -C ../src/dock  install
+First in the terminal, type the command
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-dock.cpp: In function ‘int main(int, char**)’:
-dock.cpp:340:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool, bool, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
-|     while (c_library.get_mol(mol, false, false, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
-      |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)
-In file included from dock.cpp:62:
-library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
-|     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
-      |                     ^12:36, 21 February 2025 (EST)~
-library_file.h:141:21: note:   candidate expects 7 arguments, 8 provided
-dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
-|     while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
-      |            12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
-library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
-|     bool            get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
-      |                     ^12:36, 21 February 2025 (EST)~
-library_file.h:141:21: note:   candidate expects 7 arguments, 8 provided
-make[1]: *** [../../install/rules.h:36: dock.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn051 install]$ cd ..
-(base) [ehspector@dn051 alpha_branch]$ cd ..
-(base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
-(base) [ehspector@dn051 dock]$ vi library_file.h
-(base) [ehspector@dn051 dock]$ cd ../../install/
-(base) [ehspector@dn051 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn051 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 17 13:45:32 EST 2025.
-make -C ../src/dock  install
+    vi 1O86_ligand_Du.mol2
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fingerprint.h:13,
-                 from fingerprint.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fingerprint.h:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fraggraph.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fraggraph.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fragment.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from gasteiger.h:8,
-                 from gasteiger.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from gasteiger.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from hungarian.h:7,
-                 from hungarian.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from hungarian.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from library_file.h:9,
-                 from library_file.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from library_file.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-library_file.cpp: In member function ‘void Library_File::open_files()’:
-library_file.cpp:1384:21: error: no matching function for call to ‘Library_File::read_mol(DOCKMol&, bool’
-|         if (read_mol(tmp_mol, false))
-      |             12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)
-library_file.h:139:21: note: candidate: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’
-|     bool            read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
-      |                     ^12:36, 21 February 2025 (EST)~~
-library_file.h:139:21: note:   candidate expects 3 arguments, 2 provided
-library_file.cpp: At global scope:
-library_file.cpp:1435:1: error: no declaration matches ‘bool Library_File::read_mol(DOCKMol&, bool)’
-| Library_File::read_mol(DOCKMol & mol, bool read_amber)
-      | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
-library_file.h:139:21: note: candidate is: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’
-|     bool            read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
-      |                     ^12:36, 21 February 2025 (EST)~~
-library_file.h:19:17: note: ‘class Library_File’ defined here
-| class           Library_File:public Base_MPI {
-      |                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
-make[1]: *** [../../install/rules.h:36: library_file.o] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn051 install]$ cd ..
-(base) [ehspector@dn051 alpha_branch]$ cd src/dock
-(base) [ehspector@dn051 dock]$ vi dock.cpp
-(base) [ehspector@dn051 dock]$ vi library_file.cpp
-(base) [ehspector@dn051 dock]$ cd ../../install/
-(base) [ehspector@dn051 install]$ make clean
-make -C ../src  clean
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-make -C dock  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-/bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
-cd nab && make clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-/bin/rm -f *.o nab.a lex.mm_options.c
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make cleanall
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-/bin/rm -f *.o libgzstream.a test_gzip test_gunzip
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make -C accessories  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-/bin/rm -f showbox.o showsphere.o sphgen.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
-make -C gbsa_grids  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C schemgrid_GB  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
-make -C schemgrid_SA  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-/bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
-make -C grid  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-/bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
-make -C tleap  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-/bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
-make -C antechamber  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-/bin/rm -f *.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
-make -C mopac6/src  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-/bin/rm -f aababc.o  readmo.o writmo.o mopac.o analyt.o anavib.o  axis.o  block.o  bonds.o  brlzon.o  calpar.o capcor.o  cdiag.o  chrge.o  cnvg.o  compfg.o  datin.o dcart.o  delmol.o  delri.o  denrot.o  densit.o  depvar.o deri0.o  deri1.o  deri2.o  deri21.o  deri22.o  deri23.o deritr.o  deriv.o  dernvo.o  ders.o  dfock2.o  dfpsav.o diag.o  diat.o  diat2.o  diis.o  dijkl1.o  dijkl2.o dipind.o  dipole.o  dofs.o  dot.o  drc.o  drcout.o ef.o  enpart.o  exchng.o  ffhpol.o  flepo.o  fmat.o fock1.o  fock2.o  force.o  formxy.o  forsav.o  frame.o freqcy.o  geout.o  geoutg.o  getgeg.o  getgeo.o  getsym.o gettxt.o  gmetry.o  gover.o  grid.o  h1elec.o  haddon.o hcore.o  helect.o  hqrii.o  ijkl.o  interp.o  iter.o jcarin.o  linmin.o  local.o  locmin.o  mamult.o  matout.o matpak.o  meci.o  mecid.o  mecih.o  mecip.o  moldat.o molval.o  mullik.o  mult.o  nllsq.o  nuchar.o  parsav.o partxy.o  pathk.o  paths.o  perm.o  polar.o  powsav.o powsq.o  prtdrc.o  quadr.o  react1.o  reada.o  refer.o repp.o  rotat.o  rotate.o  rsp.o  search.o  second.o setupg.o  solrot.o  swap.o  symtry.o  thermo.o  timer.o update.o  vecprt.o  wrtkey.o  wrttxt.o  xyzint.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
-make -C resp  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-/bin/rm -f amopen.o lapack.o mexit.o resp.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
-make -C docktools  clean
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make -C chemgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
-make -C solvgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-/bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
-make -C solvgrids_sev  clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-/bin/rm -f sas.o cube.o memalloc.o solvmap.o
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
-make -C convgrids      clean
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridconv.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make -f gridrdsl.mk clean
-make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-/bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
-make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
-(base) [ehspector@dn051 install]$ make dock
-Starting installation of
-DOCK v6.12
-program dock at Mon Feb 17 13:53:32 EST 2025.
-make -C ../src/dock  install
+Or, open the Mol2 file in your text editor of choice.
-make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o  amber_typer.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from amber_typer.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from amber_typer.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o  base_grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o  base_mpi.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_mpi.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
-                 from base_mpi.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o  base_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from base_score.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from base_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o  conf_gen_ag.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ag.h:5,
-                 from conf_gen_ag.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ag.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o  conf_gen_cg.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_cg.h:5,
-                 from conf_gen_cg.cpp:17:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_cg.cpp:8:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o  conf_gen_dn.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn.h:12,
-                 from conf_gen_dn.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o  conf_gen_dn_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_dn_ga.h:12,
-                 from conf_gen_dn_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_dn_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o  conf_gen_ga.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_ga.h:13,
-                 from conf_gen_ga.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from conf_gen_ga.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o  conf_gen_hdb.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from conf_gen_hdb.h:4,
-                 from conf_gen_hdb.cpp:14:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from conf_gen_hdb.cpp:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o  dock.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from dock.cpp:61:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dock.cpp:53:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o  dockmol.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from dockmol.cpp:37:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from dockmol.cpp:33:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o  filter.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from filter.h:10,
-                 from filter.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from filter.h:4:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o  fingerprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fingerprint.h:13,
-                 from fingerprint.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fingerprint.h:6:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o  fraggraph.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fraggraph.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fraggraph.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o  fragment.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.cpp:3:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from fragment.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o  gasteiger.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from gasteiger.h:8,
-                 from gasteiger.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from gasteiger.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o  grid.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o  hungarian.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from hungarian.h:7,
-                 from hungarian.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from hungarian.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o  library_file.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from library_file.h:9,
-                 from library_file.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from library_file.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o  limit_max_change.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from limit_max_change.h:12,
-                 from limit_max_change.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from limit_max_change.h:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o  master_conf.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from master_conf.h:6,
-                 from master_conf.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from master_conf.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o  master_score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from master_score.cpp:2:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from master_score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o  orient.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from orient.h:7,
-                 from orient.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from orient.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o  sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from sasa.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from sasa.h:14:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o  score.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o  score_amber.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_amber.cpp:66:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_amber.cpp:55:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o  score_chemgrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_chemgrid.cpp:39:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
-                 from score_chemgrid.cpp:38:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o  score_descriptor.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_descriptor.cpp:10:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_descriptor.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o  score_footprint.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_footprint.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_footprint.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o  score_ph4.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_ph4.h:7,
-                 from score_ph4.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_ph4.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o  score_volume.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_volume.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_volume.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o  score_gist.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_gist.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_gist.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o  score_hbond.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_hbond.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_hbond.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o  score_internal.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_internal.cpp:8:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_internal.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o  score_multigrid.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score_multigrid.cpp:9:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_multigrid.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o  score_sasa.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_sasa.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_sasa.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o  score_solvent.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from score_solvent.h:9,
-                 from sasa.h:15,
-                 from score_solvent.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from score_solvent.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o  simplex.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from score.h:7,
-                 from master_score.h:5,
-                 from simplex.cpp:4:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from simplex.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o  sphere.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o  trace.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o  utils.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from utils.cpp:7:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from utils.cpp:1:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o  iso_align.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from fragment.h:12,
-                 from iso_align.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
-                 from fragment.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o  mem_info.cpp
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o  rdtyper.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
-                 from rdtyper.cpp:18:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
-                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
-                 from rdtyper.cpp:2:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o  rddrive.cpp
-In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
-                 from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
-                 from dockmol.h:16,
-                 from rddrive.cpp:1:
-/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
-|         struct hash_base : std::unary_function<T, std::size_t> {};
-      |                                 ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
-                 from dockmol.h:5:
-/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
-|     struct unary_function
-      |            ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
-cd nab && make all
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-gcc -c -O3 -D_ANSI_SOURCE  molio.c
-gcc -c  -O2 -o prm.o  prm.c
-make is_LEX_available
-make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
-gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600  sff.c
-gcc -c  -O2 -o traceback.o  traceback.c
-gcc -c  -O2 -o select_atoms.o  select_atoms.c
-gcc -c  -O2 -o memutil.o  memutil.c
-gcc -c  -O2 -o reslib.o  reslib.c
-gcc -c  -O2 -o jacobi.o  jacobi.c
-gcc -c  -O2 -o molutil.o  molutil.c
-gcc -c  -O2 -o chirvol.o  chirvol.c
-gcc -c  -O2 -o regexp.o  regexp.c
-gcc -c  -O2 -o binpos.o  binpos.c
-gcc -c  -O2 -o time.o  time.c
-gcc -c -O3 -D_ANSI_SOURCE  rand2.c
-gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
-gcc -c  -O2 -o database.o  database.c
-gcc -c  -O2 -o tleap.o  tleap.c
-ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
-ar: creating nab.a
-a - molio.o
-a - prm.o
-a - sff.o
-a - traceback.o
-a - select_atoms.o
-a - memutil.o
-a - reslib.o
-a - jacobi.o
-a - molutil.o
-a - chirvol.o
-a - regexp.o
-a - binpos.o
-a - time.o
-a - rand2.o
-a - conjgrad.o
-a - database.o
-a - tleap.o
-ranlib nab.a
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
-cd gzstream && make
-make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
-ar cr libgzstream.a gzstream.o
-make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
-g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
-	-L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
-conf_gen_dn.o: In function `DN_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
-conf_gen_dn.cpp:(.text+0x1ec40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
-conf_gen_dn.o: In function `DN_Build::read_library_anchor(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
-conf_gen_dn.cpp:(.text+0x1f508): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
-conf_gen_dn_ga.o: In function `DN_GA_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
-conf_gen_dn_ga.cpp:(.text+0xdf40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
-conf_gen_ga.o: In function `GA_Recomb::read_library(std::vector<DOCKMol, std::allocator<DOCKMol> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
-conf_gen_ga.cpp:(.text+0x1d5c5): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
-fingerprint.o: In function `Fingerprint::input_parameters(Parameter_Reader&)':
-fingerprint.cpp:(.text+0x2f14): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
-library_file.o:library_file.cpp:(.text+0x6c75): more undefined references to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' follow
-collect2: error: ld returned 1 exit status
-make[1]: *** [Makefile:39: dock6.rdkit] Error 1
-make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
-make: *** [Makefile:28: dock] Error 2
-(base) [ehspector@dn051 install]$ exiy
-bash: exiy: command not found
-(base) [ehspector@dn051 install]$ exit
-exit
-srun: error: dn051: task 0: Exited with exit code 127
-(base) [ehspector@milan1 dock]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+Find the C9 atom and modify the atom type. Your input file should look like this:
-. Duo Push to XXX-XXX-9204
+[[File:Input_file.png|600px]]
-Passcode or option (1-1): 1
+Save it.
-Pushed a login request to your device...
+Now lets verify this change by opening the mol2 file on Chimera:
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ mkdir test
-(base) [ehspector@milan1 AMS_536]$ mkdir test
-mkdir: cannot create directory ‘test’: File exists
-(base) [ehspector@milan1 AMS_536]$ mkdir move
-(base) [ehspector@milan1 AMS_536]$ mv test/ move/
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  move  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ rm -r move
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd class_project/
-(base) [ehspector@milan1 class_project]$ ls
-(base) [ehspector@milan1 class_project]$ cd T
--bash: cd: T: No such file or directory
-(base) [ehspector@milan1 class_project]$ ls
-(base) [ehspector@milan1 class_project]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  test4.tar
-_surface_spheres  005_dock       008_cartesian_min   Robs_2w26
-_gridbox          006_footprint  009_rescore         Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan1 Robs_new_2w26]$ ls
-_test       002_spheres  004_dock      006_ga_lib
-_structure  003_grid     005_analysis  007_ga_run1
-(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan1 2w26]$ mkdir ga_calc
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_new_2w26
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               test4.tar
-_gridbox          006_footprint  009_rescore         Robs_2w26
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ vi N
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
-(base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan1 Robs_new_2w26]$ ls
-_test       002_spheres  004_dock      006_ga_lib
-_structure  003_grid     005_analysis  007_ga_run1
-(base) [ehspector@milan1 Robs_new_2w26]$ cd 006_ga_lib/
-(base) [ehspector@milan1 006_ga_lib]$ ls
-lib.sh                  2W26.fraglib.out             2W26_fragout_scored.mol2
-combine.sh              2W26_fraglib_rigid.mol2      full_fraglib.dat
-W26.fraglib.in           2W26_fraglib_scaffold.mol2   full_sorted_fraglib.dat
-W26_fraglib_linker.mol2  2W26_fraglib_sidechain.mol2  unique_full_sorted_fraglib.dat
-W26.fraglib.log          2W26_fraglib_torenv.dat
-(base) [ehspector@milan1 006_ga_lib]$ vi 2W26.fraglib.in
-(base) [ehspector@milan1 006_ga_lib]$ cd ..
-(base) [ehspector@milan1 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/006_ga_lib/2W26.fraglib.in ga_calc/2w26_fraglib.in
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_new_2w26
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               test4.tar
-_gridbox          006_footprint  009_rescore         Robs_2w26
-(base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
-(base) [ehspector@milan1 007_virtual_screen]$ ls
-virtual.in  virtual.out  virtual_scored.mol2  virtual.sh  vs_output.txt
-(base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
-(base) [ehspector@milan1 007_virtual_screen]$ cd ..
-(base) [ehspector@milan1 2w26]$ cp 004_energymin/min.sh ga_calc/lib.sh
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_new_2w26
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               test4.tar
-_gridbox          006_footprint  009_rescore         Robs_2w26
-(base) [ehspector@milan1 2w26]$ cd ga_calc/
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in  lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
-(base) [ehspector@milan1 ga_calc]$ cd ../001_structure/
-(base) [ehspector@milan1 001_structure]$ ls
-w26_ligand_H_cH.mol2      2w26_protein_H_cH.mol2
-w26_ligand_noH_nocH.mol2  2w26_protein_noH_nocH.mol2
-(base) [ehspector@milan1 001_structure]$ cd ../ga_calc/
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in  lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
-(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
-(base) [ehspector@milan1 ga_calc]$ bash lib.sh
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in           2W26_fraglib_rigid.mol2     2W26_fraglib_sidechain.mol2
-W26_fraglib_linker.mol2  2W26_fraglib_scaffold.mol2  2W26_fraglib_torenv.dat
-w26_fraglib.out          2w26_fraglib_scored.mol2    lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.out
-(base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_scaffold.mol2
-(base) [ehspector@milan1 ga_calc]$ grep -c "lnk" 2W26_fraglib_linker.mol2
-(base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_linker.mol2
-(base) [ehspector@milan1 ga_calc]$ vi py.sh
-(base) [ehspector@milan1 ga_calc]$ vi lib.sh.sh
-(base) [ehspector@milan1 ga_calc]$ vi lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi py.sh
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in           2W26_fraglib_rigid.mol2     2W26_fraglib_sidechain.mol2  py.sh
-W26_fraglib_linker.mol2  2W26_fraglib_scaffold.mol2  2W26_fraglib_torenv.dat
-w26_fraglib.out          2w26_fraglib_scored.mol2    lib.sh
-(base) [ehspector@milan1 ga_calc]$ vi py.sh
-(base) [ehspector@milan1 ga_calc]$ module load python
-(base) [ehspector@milan1 ga_calc]$ bash py.sh
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
-W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
-w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
-W26_fraglib_rigid.mol2     full_fraglib.dat
-W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
-(base) [ehspector@milan1 ga_calc]$ cd ..
-(base) [ehspector@milan1 2w26]$ mkdir ga_run
-(base) [ehspector@milan1 2w26]$ cd ga_run/
-(base) [ehspector@milan1 ga_run]$ ls
-(base) [ehspector@milan1 ga_run]$ touch 2w26_ga.in
-(base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in
+[[File:New_dummy_Ligand.png|600px]]
+As you can see C9 is now a dummy atom as shown in purple
---------------------------------------
+Now, the Mol2 is ready for De Novo calculations
-DOCK v6.12
-Released September 2024
+As a last step, transfer the mol2 to your working directory on Seawulf
-Copyright UCSF
---------------------------------------
+  scp 1O86_ligand_Du.mol2 yourusername@login.seawulf.stonybrook.edu:'/gpfs/home/yourusername/tutorial/010_de_novo/'
-Conformational Sampling Parameters
+=== Running The Denovo Calculation ===
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic
-Genetic Algorithm Recombination Parameters
+In your 010_De_Novo folder create an empty input file:
-------------------------------------------------------------------------------------------
-                                             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
+   touch DN.in
-------------------------------------------------------------------------------------------
-                                          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
+Then prompt the question tree with the dock program:
-------------------------------------------------------------------------------------------
-                                          use_database_filter [no] (yes no):
-Orient Ligand Parameters
+   dock6 -i DN.in
-------------------------------------------------------------------------------------------
-                                                orient_ligand [yes] (yes no):no
-Bump Filter Parameters
+Follow the question tree and use the following sample input file as a template
-------------------------------------------------------------------------------------------
-                                                  bump_filter [no] (yes no):
-Master Score Parameters
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):
-Contact Score Parameters
+   conformer_search_type                                        denovo
-------------------------------------------------------------------------------------------
+   dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
-                                         contact_score_primary [no] (yes no):
+   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                                             DN.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
-Grid Score Parameters
-------------------------------------------------------------------------------------------
-                                           grid_score_primary [yes] (yes no):no
-GIST Score Parameters
+Once you've filled out the input file, you can then go ahead and run the calculation
-------------------------------------------------------------------------------------------
-                                           gist_score_primary [no] (yes no):
-MultiGrid Score Parameters
+   dock6 -i DN.in -o DN.out
-------------------------------------------------------------------------------------------
-                                      multigrid_score_primary [no] (yes no):
-Dock3.5 Score Parameters
+After running the calculations, the following output files will be generated:
-------------------------------------------------------------------------------------------
-                                        dock3.5_score_primary [no] (yes no):
+  DN.out
+  DN.out.anchor_1.root_layer_1.mol
+  DN.out.completed.denovo_build.mol2
+  DN.out.denovo_build.mol2
-Continuous Energy Score Parameters
+Examining the output file you can see how many molecules were grown.
-------------------------------------------------------------------------------------------
-                                     continuous_score_primary [no] (yes no):
-Footprint Similarity Score Parameters
+[[File:Attach_out.png|600px]]
-------------------------------------------------------------------------------------------
-                           footprint_similarity_score_primary [no] (yes no):
-Pharmacophore Similarity Score Parameters
+In this case there are 21 different attached molecules.
-------------------------------------------------------------------------------------------
-                                  pharmacophore_score_primary [no] (yes no):
-Hbond Energy Score Parameters
+Now, copy over the DN.out.completed.denovo_build.mol2 to your home computer
-------------------------------------------------------------------------------------------
-                                          hbond_score_primary [no] (yes no):
-Internal Energy Score Parameters
+    scp yourusername@login.seawulf.stonybrook.edu:'/gpfs/home/yourusername/tutorial/010_de_novo/DN.out.completed.denovo_build.mol2' .
-------------------------------------------------------------------------------------------
-                                internal_energy_score_primary [no] (yes no):
-Descriptor Score Parameters
+=== Visualizing the Molecules in Chimera ===
-------------------------------------------------------------------------------------------
-                                     descriptor_score_primary [no] (yes no):
-Zou GB/SA Score Parameters
+Head over to Chimera and go to Tools >> Surface/Binding Analysis >> Scroll down to where you see ViewDock and select it
-------------------------------------------------------------------------------------------
-                                       gbsa_zou_score_primary [no] (yes no):
-Hawkins GB/SA Score Parameters
+Then select the DN.out.completed_denovo.mol2
-------------------------------------------------------------------------------------------
-                                   gbsa_hawkins_score_primary [no] (yes no):
-SASA Score Parameters
+The following menu will appear:
-------------------------------------------------------------------------------------------
-                                           SASA_score_primary [no] (yes no):
-Amber Score Parameters
+[[File:View_Dock.png|600px]]
-------------------------------------------------------------------------------------------
-                                          amber_score_primary [no] (yes no):
-Error:  No scoring function selected for the primary score.  Program will now terminate.
+You can navigate through the list of molecules that were grown from the calculations.
-(base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in
+You'll notice that the best scoring ligand retained the oxygens from the original ligand:
-(base) [ehspector@milan1 ga_run]$ ls
-w26_ga.in
-(base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in
-(base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in
+[[File:Best_Scoring_Ligand.png|600px]]
+Opening the original ligand mol2, you'll see that the molecules are almost identical
---------------------------------------
+[[File:Overlap_Ligand.png|600px]]
-DOCK v6.12
-Released September 2024
+If you return to the ViewDock menu and highlight all of the ligands.
-Copyright UCSF
+You will be able to see a depiction of all of the different refinements.
---------------------------------------
+This can be done by going to Tools >> ViewDock >> Raise
+Now that the menu has been prompted hold down your shift key and select the first ligand,
+then scroll down and select the last ligand. All your molecules will be shown overlapping on Chimera:
-Conformational Sampling Parameters
+[[File:Refinements.png|600px]]
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic
-Genetic Algorithm Recombination Parameters
+Well done, you've now completed a simple denovo calculation!
-------------------------------------------------------------------------------------------
-                                             ga_molecule_file [ga_molecule_file.mol2] ():^C
-(base) [ehspector@milan1 ga_run]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_2w26
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_new_2w26
-_gridbox          006_footprint  009_rescore         ga_run                test4.tar
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ bash commands.txt
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  protein  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd protein/
-(base) [ehspector@milan1 protein]$ ls
-_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min
-(base) [ehspector@milan1 protein]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ rm -r protein/
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  Robs_2w26
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_new_2w26
-_gridbox          006_footprint  009_rescore         ga_run                test4.tar
-(base) [ehspector@milan1 2w26]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+== Running a Generic De Novo Calculation ==
-. Duo Push to XXX-XXX-9204
+In this part of the tutorial, you will be running a '''generic denovo calculation'''.
+What this means is that you take an anchor, or don't specify one, and grow a ligand around parts of the molecule.
+These parts of the molecule are dictated by the selected spheres that were calculated in the second part of the VS tutorial.
+The end result becomes a series of newly 'grown' ligands based on the user defined parameters. These parameters are what will bias
+the denovo growth to meet a certain criterian (i.e. a specific molecular weight). For this tutorial, you will select an anchor and use that
+to grow a series of ligands, which you will then be able to see on chimera.
-Passcode or option (1-1): 1
+To start, lets create a new directory in your <code> 010_de_novo </code> directory.
+Lets call it generic.
-Pushed a login request to your device...
+    mkdir generic
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan2 ~]$ cd AMS_536/
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run/
-(base) [ehspector@milan2 ga_run]$ ls
-w26_ga.in  2w26_ga_lib.in
-(base) [ehspector@milan2 ga_run]$ vi 2w26_ga_lib.in
-(base) [ehspector@milan2 ga_run]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd Robs_new_2w26/
-(base) [ehspector@milan2 Robs_new_2w26]$ cd 007_ga_run1/
-(base) [ehspector@milan2 007_ga_run1]$ ls
-W26_ga.in   2W26_ga.restart0000.mol2  2W26_ga.restart0002.mol2  2W26_ga.restart0004.mol2
-W26_ga.out  2W26_ga.restart0001.mol2  2W26_ga.restart0003.mol2  2W26_ga.restart0005.mol2
-(base) [ehspector@milan2 007_ga_run1]$ vi 2W26_ga.in
-(base) [ehspector@milan2 007_ga_run1]$ cd ..
-(base) [ehspector@milan2 Robs_new_2w26]$ ls
-_test  001_structure  002_spheres  003_grid  004_dock  005_analysis  006_ga_lib  007_ga_run1
-(base) [ehspector@milan2 Robs_new_2w26]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ga_run/
-(base) [ehspector@milan2 ga_run]$ ls
-w26_ga.in  2w26_ga_lib.in
-(base) [ehspector@milan2 ga_run]$ rm 2w26_ga_lib.in
-(base) [ehspector@milan2 ga_run]$ vi 2w26_ga.in
-(base) [ehspector@milan2 ga_run]$ rm 2w26_ga.in
-(base) [ehspector@milan2 ga_run]$ cd ..
-(base) [ehspector@milan2 2w26]$ cp Robs_new_2w26/007_ga_run1/2W26_ga.in ga_calc/2w26_ga.in
-(base) [ehspector@milan2 2w26]$ mv ga_calc/2w26_ga.in ga_run/
-(base) [ehspector@milan2 2w26]$ mv ga_run/ ga_run_5
-(base) [ehspector@milan2 2w26]$ mkdir ga_run_50
-(base) [ehspector@milan2 2w26]$ cd ga_run_5
-(base) [ehspector@milan2 ga_run_5]$ ls
-w26_ga.in
-(base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in
-(base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out
-(base) [ehspector@milan2 ga_run_5]$ ls
-w26_ga.in  2w26_ga.out
-(base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.out
-(base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in
-(base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out
-(base) [ehspector@milan2 ga_run_5]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0002.mol2  2w26_5_ga.restart0004.mol2  2w26_ga.in
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0005.mol2  2w26_ga.out
-(base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.in 2w26_ga_5.in
-(base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.out 2w26_ga_5.out
-(base) [ehspector@milan2 ga_run_5]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0002.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_5.in
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0005.mol2  2w26_ga_5.out
-(base) [ehspector@milan2 ga_run_5]$ cd ..
-(base) [ehspector@milan2 2w26]$ cp ga_run_5/2w26_ga_5.in ga_run_50/2w26_ga_50.in
-(base) [ehspector@milan2 2w26]$ cp 007_virtual_screen/virtual.sh ga_run_50/ga.sh
-(base) [ehspector@milan2 2w26]$ cd ga_run_50
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_ga_50.in  ga.sh
-(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
-(base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
-(base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
-(base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
-(base) [ehspector@milan2 ga_run_50]$ avail
-PARTITION              AVAIL  TIMELIMIT  NODES  STATE NODELIST
-a100                      up    8:00:00      2   mix@ a100-[02,04]
-a100                      up    8:00:00      8 alloc@ a100-[03,05-11]
-a100                      up    8:00:00      1 drain* a100-01
-a100-large                up    8:00:00      2   mix@ a100-[02,04]
-a100-large                up    8:00:00      8 alloc@ a100-[03,05-11]
-a100-large                up    8:00:00      1 drain* a100-01
-a100-long                 up 2-00:00:00      2   mix@ a100-[02,04]
-a100-long                 up 2-00:00:00      8 alloc@ a100-[03,05-11]
-a100-long                 up 2-00:00:00      1 drain* a100-01
-debug-40core              up    1:00:00      2 drain* dn[031,037]
-debug-40core              up    1:00:00      1  drain dn061
-debug-40core              up    1:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-debug-40core              up    1:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-extended-40core           up 7-00:00:00      2 drain* dn[031,037]
-extended-40core           up 7-00:00:00      1  drain dn061
-extended-40core           up 7-00:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-extended-40core           up 7-00:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-extended-40core-shared    up 3-12:00:00      2 drain* dn[031,037]
-extended-40core-shared    up 3-12:00:00      1  drain dn061
-extended-40core-shared    up 3-12:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-extended-40core-shared    up 3-12:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-extended-96core           up 7-00:00:00      1   plnd dg025
-extended-96core           up 7-00:00:00      1  drng@ dg023
-extended-96core           up 7-00:00:00      1   mix@ dg039
-extended-96core           up 7-00:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-extended-96core           up 7-00:00:00      1  down* dg009
-extended-96core           up 7-00:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-extended-96core-shared    up 3-12:00:00      1   plnd dg025
-extended-96core-shared    up 3-12:00:00      1  drng@ dg023
-extended-96core-shared    up 3-12:00:00      1   mix@ dg039
-extended-96core-shared    up 3-12:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-extended-96core-shared    up 3-12:00:00      1  down* dg009
-extended-96core-shared    up 3-12:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-hbm-1tb-long-96core       up 2-00:00:00      3  alloc xm[046-048]
-hbm-1tb-long-96core       up 2-00:00:00      1   idle xm045
-hbm-extended-96core       up 7-00:00:00      3   plnd xm[008,021,088]
-hbm-extended-96core       up 7-00:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
-hbm-extended-96core       up 7-00:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
-hbm-large-96core          up    8:00:00      3   plnd xm[008,021,088]
-hbm-large-96core          up    8:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
-hbm-large-96core          up    8:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
-hbm-long-96core           up 2-00:00:00      3   plnd xm[008,021,088]
-hbm-long-96core           up 2-00:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
-hbm-long-96core           up 2-00:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
-hbm-medium-96core         up   12:00:00      3   plnd xm[008,021,088]
-hbm-medium-96core         up   12:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
-hbm-medium-96core         up   12:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
-hbm-short-96core          up    4:00:00      3   plnd xm[008,021,088]
-hbm-short-96core          up    4:00:00      9 alloc@ xm[016,019,028-029,031,037,054,081-082]
-hbm-short-96core          up    4:00:00     78  alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
-large-40core              up    8:00:00      2 drain* dn[031,037]
-large-40core              up    8:00:00      1  drain dn061
-large-40core              up    8:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-large-40core              up    8:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-large-96core              up    8:00:00      1   plnd dg025
-large-96core              up    8:00:00      1  drng@ dg023
-large-96core              up    8:00:00      1   mix@ dg039
-large-96core              up    8:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-large-96core              up    8:00:00      1  down* dg009
-large-96core              up    8:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-long-40core               up 2-00:00:00      2 drain* dn[031,037]
-long-40core               up 2-00:00:00      1  drain dn061
-long-40core               up 2-00:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-long-40core               up 2-00:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-long-40core-shared        up 1-00:00:00      2 drain* dn[031,037]
-long-40core-shared        up 1-00:00:00      1  drain dn061
-long-40core-shared        up 1-00:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-long-40core-shared        up 1-00:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-long-96core               up 2-00:00:00      1   plnd dg025
-long-96core               up 2-00:00:00      1  drng@ dg023
-long-96core               up 2-00:00:00      1   mix@ dg039
-long-96core               up 2-00:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-long-96core               up 2-00:00:00      1  down* dg009
-long-96core               up 2-00:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-long-96core-shared        up 1-00:00:00      1   plnd dg025
-long-96core-shared        up 1-00:00:00      1  drng@ dg023
-long-96core-shared        up 1-00:00:00      1   mix@ dg039
-long-96core-shared        up 1-00:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-long-96core-shared        up 1-00:00:00      1  down* dg009
-long-96core-shared        up 1-00:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-medium-40core             up   12:00:00      2 drain* dn[031,037]
-medium-40core             up   12:00:00      1  drain dn061
-medium-40core             up   12:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-medium-40core             up   12:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-medium-96core             up   12:00:00      1   plnd dg025
-medium-96core             up   12:00:00      1  drng@ dg023
-medium-96core             up   12:00:00      1   mix@ dg039
-medium-96core             up   12:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-medium-96core             up   12:00:00      1  down* dg009
-medium-96core             up   12:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-ood-short-96core          up    4:00:00      1   idle dg038
-rn-long-40core            up 8-08:00:00     12   idle rn[001-012]
-short-40core              up    4:00:00      2 drain* dn[031,037]
-short-40core              up    4:00:00      1  drain dn061
-short-40core              up    4:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-short-40core              up    4:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-short-40core-shared       up    4:00:00      2 drain* dn[031,037]
-short-40core-shared       up    4:00:00      1  drain dn061
-short-40core-shared       up    4:00:00     10    mix dn[020-021,041-043,052-053,056,059-060]
-short-40core-shared       up    4:00:00     49  alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
-short-96core              up    4:00:00      1   plnd dg025
-short-96core              up    4:00:00      1  drng@ dg023
-short-96core              up    4:00:00      1   mix@ dg039
-short-96core              up    4:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-short-96core              up    4:00:00      1  down* dg009
-short-96core              up    4:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-short-96core-shared       up    4:00:00      1   plnd dg025
-short-96core-shared       up    4:00:00      1  drng@ dg023
-short-96core-shared       up    4:00:00      1   mix@ dg039
-short-96core-shared       up    4:00:00      8 alloc@ dg[006,010-011,014-015,019,030,040]
-short-96core-shared       up    4:00:00      1  down* dg009
-short-96core-shared       up    4:00:00     35  alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
-(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
+=== Selecting an Anchor ===
-Press ENTER or type command to continue
+Now that you have a working directory for this calculation, lets go ahead and create an anchor
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_ga_50.in  ga.sh
-(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
-(base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
-Submitted batch job 932640
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ ^C
-(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
-(base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
-Submitted batch job 932642
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-short-96c 2w26_ga_ ehspecto PD       0:00      3 (Resources)
-(base) [ehspector@milan2 ga_run_50]$ scancel 932640
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto PD       0:00      3 (PartitionNodeLimit)
-(base) [ehspector@milan2 ga_run_50]$ scancel 932642
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_ga_50.in  ga.sh
-(base) [ehspector@milan2 ga_run_50]$ vi ga.sh
-(base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
-Submitted batch job 932644
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto  R       0:03      1 dg038
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto  R       0:07      1 dg038
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0003.mol2  2w26_ga_50.in   vs_output.txt
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_50.out
-w26_5_ga.restart0002.mol2  2w26_5_ga.restart0005.mol2  ga.sh
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0006.mol2  ga.sh
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_50.in               vs_output.txt
-w26_5_ga.restart0002.mol2  2w26_5_ga.restart0005.mol2  2w26_ga_50.out
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0003.mol2  2w26_5_ga.restart0006.mol2  ga.sh
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0004.mol2  2w26_ga_50.in               vs_output.txt
-w26_5_ga.restart0002.mol2  2w26_5_ga.restart0005.mol2  2w26_ga_50.out
-(base) [ehspector@milan2 ga_run_50]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto  R       0:41      1 dg038
-(base) [ehspector@milan2 ga_run_50]$ exit
-logout
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+file to run the generic denovo calculation. For our anchor of choice, we will use the most popular
-. Duo Push to XXX-XXX-9204
+sidechain from dock6's current library. To start off, copy the library mol2 file to your home directory from
-Passcode or option (1-1): 1
+seawulf:
-Pushed a login request to your device...
+     scp yourusername@milan.seawulf.stonybrook.edu:'/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2' .
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ class
-(base) [ehspector@milan2 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan2 AMS_536]$ check
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-ood-short 2w26_ga_ ehspecto  R       8:17      1 dg038
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  ga_run_50      test4.tar
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_2w26
-_gridbox          006_footprint  009_rescore         ga_run_5              Robs_new_2w26
-(base) [ehspector@milan2 2w26]$ cd ga_run_50/
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0008.mol2  2w26_5_ga.restart0016.mol2
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0009.mol2  2w26_5_ga.restart0017.mol2
-w26_5_ga.restart0002.mol2  2w26_5_ga.restart0010.mol2  2w26_5_ga.restart0018.mol2
-w26_5_ga.restart0003.mol2  2w26_5_ga.restart0011.mol2  2w26_ga_50.in
-w26_5_ga.restart0004.mol2  2w26_5_ga.restart0012.mol2  2w26_ga_50.out
-w26_5_ga.restart0005.mol2  2w26_5_ga.restart0013.mol2  ga.sh
-w26_5_ga.restart0006.mol2  2w26_5_ga.restart0014.mol2  vs_output.txt
-w26_5_ga.restart0007.mol2  2w26_5_ga.restart0015.mol2
-(base) [ehspector@milan2 ga_run_50]$ exit
-logout
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+It's a pretty hefty file and the way you are going to open the file is by using ViewDock on Chimera.
-. Duo Push to XXX-XXX-9204
+Navigate to Chimera and select Tools --> Surface/Binding Analysis --> View Dock
-Passcode or option (1-1): 1
+Select the fraglib_sidechain.mol2 file.
-Pushed a login request to your device...
+On chimera you'll see a methyl-ethyl sidechain popup and the View Dock menu to toggle through other sidechains:
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan2 ~]$ cd AMS_536/
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run_50/
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_5_ga.restart0000.mol2  2w26_5_ga.restart0019.mol2  2w26_5_ga.restart0038.mol2
-w26_5_ga.restart0001.mol2  2w26_5_ga.restart0020.mol2  2w26_5_ga.restart0039.mol2
-w26_5_ga.restart0002.mol2  2w26_5_ga.restart0021.mol2  2w26_5_ga.restart0040.mol2
-w26_5_ga.restart0003.mol2  2w26_5_ga.restart0022.mol2  2w26_5_ga.restart0041.mol2
-w26_5_ga.restart0004.mol2  2w26_5_ga.restart0023.mol2  2w26_5_ga.restart0042.mol2
-w26_5_ga.restart0005.mol2  2w26_5_ga.restart0024.mol2  2w26_5_ga.restart0043.mol2
-w26_5_ga.restart0006.mol2  2w26_5_ga.restart0025.mol2  2w26_5_ga.restart0044.mol2
-w26_5_ga.restart0007.mol2  2w26_5_ga.restart0026.mol2  2w26_5_ga.restart0045.mol2
-w26_5_ga.restart0008.mol2  2w26_5_ga.restart0027.mol2  2w26_5_ga.restart0046.mol2
-w26_5_ga.restart0009.mol2  2w26_5_ga.restart0028.mol2  2w26_5_ga.restart0047.mol2
-w26_5_ga.restart0010.mol2  2w26_5_ga.restart0029.mol2  2w26_5_ga.restart0048.mol2
-w26_5_ga.restart0011.mol2  2w26_5_ga.restart0030.mol2  2w26_5_ga.restart0049.mol2
-w26_5_ga.restart0012.mol2  2w26_5_ga.restart0031.mol2  2w26_5_ga.restart0050.mol2
-w26_5_ga.restart0013.mol2  2w26_5_ga.restart0032.mol2  2w26_ga_50.in
-w26_5_ga.restart0014.mol2  2w26_5_ga.restart0033.mol2  2w26_ga_50.out
-w26_5_ga.restart0015.mol2  2w26_5_ga.restart0034.mol2  ga.sh
-w26_5_ga.restart0016.mol2  2w26_5_ga.restart0035.mol2  vs_output.txt
-w26_5_ga.restart0017.mol2  2w26_5_ga.restart0036.mol2
-w26_5_ga.restart0018.mol2  2w26_5_ga.restart0037.mol2
-(base) [ehspector@milan2 ga_run_50]$ mkdir 50_generations
-(base) [ehspector@milan2 ga_run_50]$ mv *.mol2 50_generations/
-(base) [ehspector@milan2 ga_run_50]$ ls
-w26_ga_50.in  2w26_ga_50.out  50_generations  ga.sh  vs_output.txt
-(base) [ehspector@milan2 ga_run_50]$ cd 50_generations/
-(base) [ehspector@milan2 50_generations]$ cd ..
-(base) [ehspector@milan2 ga_run_50]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ga_run_5
-(base) [ehspector@milan2 ga_run_5]$ mkdir 5_generations
-(base) [ehspector@milan2 ga_run_5]$ mv *.mol2 5_generations/
-(base) [ehspector@milan2 ga_run_5]$ ls
-w26_ga_5.in  2w26_ga_5.out  5_generations
-(base) [ehspector@milan2 ga_run_5]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tut(base) [ehspect(base) [ehspector@m(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 (base) [ehspector@milan2 Tutorials]$ (base) [ehspector@milan(base) [(base) [ehspector@mila(base) [e(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutorials]$ client_loop: send disconnect: Broken pipe
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+[[File:methyl_ethyl.png|600px]]
-. Duo Push to XXX-XXX-9204
+[[File:view_dock_frag.png|600px]]
-Passcode or option (1-1): 1
+As mentioned before, you are going to use the most popular sidechain as the anchor for this calculation.
-Pushed a login request to your device...
+On the View Dock Menu go to Column --> Show --> FREQ
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ home
-(base) [ehspector@milan1 espector]$ class
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        004_energymin  007_virtual_screen  2025_02_12a_test.tar  ga_run_50      test4.tar
-_surface_spheres  005_dock       008_cartesian_min   ga_calc               Robs_2w26
-_gridbox          006_footprint  009_rescore         ga_run_5              Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd ga_calc/
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
-W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
-w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
-W26_fraglib_rigid.mol2     full_fraglib.dat
-W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
-(base) [ehspector@milan1 ga_calc]$ vi py.sh
-(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base(base) [ehspector@milan1 ga_c(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
-W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
-w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
-W26_fraglib_rigid.mol2     full_fraglib.dat
-W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
-(base) [ehspector@milan1 ga_calc]$ ls
-w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
-W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
-w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
-W26_fraglib_rigid.mol2     full_fraglib.dat
-W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
-(base) [ehspector@milan1 ga_calc]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ cd ga_run_5
-(base) [ehspector@milan1 ga_run_5]$ cd ..
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ cd ..
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ cd ../../
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd ../../
-(base) [ehspector@milan1 ~]$ ls
-AMS_536  miniconda3  Miniconda3-latest-Linux-x86_64.sh
-(base) [ehspector@milan1 ~]$ cd AMS_536/
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd ../
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi commands.txt
-(base) [ehspector@milan1 AMS_536]$ touch make_folders
-(base) [ehspector@milan1 AMS_536]$ vi make_folders
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  make_folders  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ bash make_folders
-make_folders: line 3: folder: Is a directory
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  folder  make_folders  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd folder/
-(base) [ehspector@milan1 folder]$ ls
-(base) [ehspector@milan1 folder]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  folder  make_folders  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ rm -r folder/
-(base) [ehspector@milan1 AMS_536]$ rm make_folders
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd ..
-(base) [ehspector@milan1 ~]$ cd AMS_536/
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd ..
-(base) [ehspector@milan1 ~]$ cd ..
-(base) [ehspector@milan1 home]$ cd ..
-(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
-(base) [ehspector@milan1 bin]$ ls
-am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
-amberize_complex   espgen        nchemgrid_GB          showbox
-amberize_ligand    grid          nchemgrid_SA          showsphere
-amberize_receptor  grid-convert  parmcal               solvgrid
-antechamber        grid-convrds  parmchk               solvmap
-atomtype           make_phimap   prepare_amber.pl      sphere_selector
-bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
-chemgrid           mol2.py       prepgen               teLeap
-combine_torenv.py  mopac         resp                  tleap
-dock6              mopac.sh      respgen
-(base) [ehspector@milan1 bin]$ class
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 2w26/
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_50
-_surface_spheres  006_footprint       2025_02_12a_test.tar  Robs_2w26
-_gridbox          007_virtual_screen  ga_calc               Robs_new_2w26
-_energymin        008_cartesian_min   ga_run_5              test4.tar
-(base) [ehspector@milan1 2w26]$ mkdir de_novo
-(base) [ehspector@milan1 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_5       test4.tar
-_surface_spheres  006_footprint       2025_02_12a_test.tar  ga_run_50
-_gridbox          007_virtual_screen  de_novo               Robs_2w26
-_energymin        008_cartesian_min   ga_calc               Robs_new_2w26
-(base) [ehspector@milan1 2w26]$ cd ../../
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
--bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
--bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
-(base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/
--bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
-(base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/
--bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
-(base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
--bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ cd
-(base) [ehspector@milan1 ~]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
--bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory
-(base) [ehspector@milan1 ~]$ cd ..
-(base) [ehspector@milan1 home]$ cd ..
-(base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
-(base) [ehspector@milan1 bin]$ ls
-am1bcc             dock6.mpi     multigrid_fp_gen.py   sevsolv
-amberize_complex   espgen        nchemgrid_GB          showbox
-amberize_ligand    grid          nchemgrid_SA          showsphere
-amberize_receptor  grid-convert  parmcal               solvgrid
-antechamber        grid-convrds  parmchk               solvmap
-atomtype           make_phimap   prepare_amber.pl      sphere_selector
-bondtype           mol2bild.py   prepare_rna_amber.pl  sphgen
-chemgrid           mol2.py       prepgen               teLeap
-combine_torenv.py  mopac         resp                  tleap
-dock6              mopac.sh      respgen
-(base) [ehspector@milan1 bin]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap
-(base) [ehspector@milan1 bin]$ class
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd ..
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan1 AMS_536]$ top
-top - 15:15:15 up 1 day,  2:11, 24 users,  load average: 0.72, 1.86, 3.46
+This is the frequency in which these particular sidechains occur in the dock6 testset:
-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
+[[File:freq.png|600px]]
-minkwan   20   0  164580  90868   3072 R  99.0   0.0   0:25.66 dock6
-ehspect+  20   0   23432   4096   3072 R   1.6   0.0   0:00.30 top
-root      20   0  259340  20196  16384 S   1.0   0.0   4:53.58 NetworkManager
-eswong    20   0  295692  13164   5120 S   0.5   0.0   0:11.35 code-e54c774e0a
-hborche+  20   0 4280208 284596  82944 S   0.5   0.1   0:01.07 cpptools-srv
-root      20   0  172980  12288   9216 S   0.0   0.0   0:40.57 systemd
-root      20   0       0      0      0 S   0.0   0.0   0:00.25 kthreadd
-root       0 -20       0      0      0 I   0.0   0.0   0:00.00 rcu_gp
-root       0 -20       0      0      0 I   0.0   0.0   0:00.00 rcu_par_gp
-root       0 -20       0      0      0 I   0.0   0.0   0:00.00 slub_flushwq
-root       0 -20       0      0      0 I   0.0   0.0   0:00.00 netns
-root       0 -20       0      0      0 I   0.0   0.0   0:00.00 kworker/0:0H-events+
-root       0 -20       0      0      0 I   0.0   0.0   0:00.00 mm_percpu_wq
-root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_kthre
-root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_rude_
-root      20   0       0      0      0 I   0.0   0.0   0:00.00 rcu_tasks_trace
-root      20   0       0      0      0 S   0.0   0.0   0:00.38 ksoftirqd/0
-root      20   0       0      0      0 I   0.0   0.0   0:50.41 rcu_preempt
-root      rt   0       0      0      0 S   0.0   0.0   0:00.08 migration/0
-root     -51   0       0      0      0 S   0.0   0.0   0:00.00 idle_inject/0
-root      20   0       0      0      0 S   0.0   0.0   0:00.00 cpuhp/0
-root      20   0       0      0      0 S   0.0   0.0   0:00.00 cpuhp/1
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ cd ..
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan1 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) supremestudier@Evans-MBP Tutorial % ls
-O86		2w26		5EEN		folders.txt
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Permission denied, please try again.
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+Ironically, the methy ethyl sidechain appears to be the most popular sidechain. This will be the anchor of choice.
-. Duo Push to XXX-XXX-9204
+Go to File --> Save Mol2
-Passcode or option (1-1): 1
+Lets call it Anchor.mol2
-Pushed a login request to your device...
+Additionally, make sure that only the first model is selected in the Select Model panel like so:
-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:
+[[File:save_anch.png|600px]]
-. Duo Push to XXX-XXX-9204
+Select Save. You can also verify that there is only one sidechain in the mol2 by viewing it on the terminal
-Passcode or option (1-1): 1
+   vi Anchor.mol2
-Pushed a login request to your device...
+The file should look like this:
-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:
+[[File:vi_anch.png|600px]]
-. Duo Push to XXX-XXX-9204
+Now you can go ahead and copy this file over to the <code> generic </code> directory in seawulf
-Passcode or option (1-1): 1
+  scp Anchor.mol2 yourusername@milan.stonybrook.edu:'/gpfs/yourusername/tutorial/010_de_novo_/generic'
-Pushed a login request to your device...
+=== Running the Calculations ===
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ~]$ home
-(base) [ehspector@milan2 espector]$ ls
-K  4s0v  builds  gas_test  RDKit  segfault_test_2  sphere_test
-(base) [ehspector@milan2 espector]$ class
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/
-(base) [ehspector@milan2 2w26]$ ls
-_structure        005_dock            009_rescore           ga_run_5       test4.tar
-_surface_spheres  006_footprint       2025_02_12a_test.tar  ga_run_50
-_gridbox          007_virtual_screen  de_novo               Robs_2w26
-_energymin        008_cartesian_min   ga_calc               Robs_new_2w26
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ mkdir de_novo
-(base) [ehspector@milan2 1O86]$ cd de_novo/
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2
-(base) [ehspector@milan2 de_novo]$ touch Du.in
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in
-(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in
+Now that you're on seawulf in the <code> generic </code> directory with your Anchor.mol2 file,
+lets create the necessary files to run the generic denovo calculation.
---------------------------------------
+First, create an input file, lets call it GDN.in.
-DOCK v6.12
-Released September 2024
+Just like when running the refinement calculation, you are encouraged to create an empty input file and follow the dock6 question tree.
-Copyright UCSF
---------------------------------------
+To create an empty input file run the following command:
-Conformational Sampling Parameters
+     touch GDN.in
-------------------------------------------------------------------------------------------
-                                        conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):denovo
-De Novo Build Parameters
+Then, use dock6 to initiate the question tree:
-------------------------------------------------------------------------------------------
-                                     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
+     dock6 -i GDN.in
-------------------------------------------------------------------------------------------
-                                          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 the following sample input file as a template when navigating the question tree:
-------------------------------------------------------------------------------------------
-                                          use_database_filter [no] (yes no):
-Orient Ligand Parameters
+   conformer_search_type                                        denovo
-------------------------------------------------------------------------------------------
+   dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
-                                                orient_ligand [yes] (yes no):no
+   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                                       ../generic/Anchor.mol2
+   dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_torenv.dat
+   dn_name_identifier                                           generic
+   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                                   550.0
+   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
+   dn_write_prune_dump                                          no
+   dn_write_orients                                             no
+   dn_write_growth_trees                                        no
+   dn_output_prefix                                             generic
+   use_internal_energy                                          yes
+   internal_energy_rep_exp                                      12
+   internal_energy_cutoff                                       100.0
+   use_database_filter                                          no
+   orient_ligand                                                yes
+   automated_matching                                           yes
+   receptor_site_file                                           ../002_spheres/selected_spheres.sph
+   max_orientations                                             1000
+   critical_points                                              no
+   chemical_matching                                            no
+   use_ligand_spheres                                           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_de_novo.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
-Bump Filter Parameters
+After creating the input file, you will need to create a slurm input file to run this calculation.
-------------------------------------------------------------------------------------------
-                                                  bump_filter [no] (yes no):
-Master Score Parameters
+  vi gdn.slurm
-------------------------------------------------------------------------------------------
-                                              score_molecules [yes] (yes no):
-Contact Score Parameters
+Type the following into the slurm file:
-------------------------------------------------------------------------------------------
-                                        contact_score_primary [no] (yes no):
-Grid Score Parameters
+  #!/bin/bash
-------------------------------------------------------------------------------------------
+  #
-                                           grid_score_primary [yes] (yes no):
+  #SBATCH --job-name=1O86_generic_de_novo
-                                     grid_score_rep_rad_scale [1] ():
+  #SBATCH --output=generic_dn_output.txt
-                                         grid_score_vdw_scale [1] ():
+  #SBATCH --ntasks-per-node=24
-                                          grid_score_es_scale [1] ():
+  #SBATCH --nodes=4
-                                          grid_lig_efficiency [no] (yes no):
+  #SBATCH --time=4:00:00
-                                       grid_score_grid_prefix [grid] ():
+  #SBATCH -p short-96core
-GIST Score Parameters
+  dock6 -i GDN.in -o GDN.out
-------------------------------------------------------------------------------------------
-MultiGrid Score Parameters
+To run the calculation submit a job with the slurm file:
-------------------------------------------------------------------------------------------
-Dock3.5 Score Parameters
+    sbatch gdn.slurm
-------------------------------------------------------------------------------------------
-Continuous Energy Score Parameters
+The job itself may take awhile to finish. It is highly recommended that you check to see if your job is still running and that your .out file to see if there are any errors.
-------------------------------------------------------------------------------------------
-Footprint Similarity Score Parameters
+After the calculations have run, the following files will show up in your directory:
-------------------------------------------------------------------------------------------
+  GDN.out                             generic_dn_output.txt
+  generic.anchor_1.root_layer_1.mol2  generic.anchor_1.root_layer_5.mol2
+  generic.anchor_1.root_layer_2.mol2  generic.anchor_1.root_layer_6.mol2
+  generic.anchor_1.root_layer_3.mol2  generic.anchor_1.root_layer_7.mol2
+  generic.anchor_1.root_layer_4.mol2  generic.completed.denovo_build.mol2
+                                      generic.denovo_build.mol2
-Pharmacophore Similarity Score Parameters
+These illustrate the different layers of growth that were specified in the input file, the <code> generic.completed.denovo_build.mol2 </code> contains all of the finished molecules regardless of how many layers of growth. To view how many molecules are in this output file, type the following line in your terminal:
-------------------------------------------------------------------------------------------
+   grep -c "SMALL" generic.completed.denovo_build.mol2
-Hbond Energy Score Parameters
+You'll notice that the number of molecules in this file come out to be 2350. That's okay, go ahead and transfer this file onto your home computer:
-------------------------------------------------------------------------------------------
-Internal Energy Score Parameters
+    scp yourusername@milan.stonybrook.edu:'gpfs/yourusername/tutorial/010_de_novo/generic/generic.completed.denovo_build.mol2' .
-------------------------------------------------------------------------------------------
-Descriptor Score Parameters
+=== Visualizing The Results ===
-------------------------------------------------------------------------------------------
-Zou GB/SA Score Parameters
+To view the molecules that were grown, use the View Dock tool in Chimera.
-------------------------------------------------------------------------------------------
+The procedure is the same as when you were selecting an anchor.
+You should wait about 30 seconds as there are a large chunk of molecules being loaded into chimera.
+Once Chimera is finished loading you will see an image of a finished sidechain and the View Dock Menu:
-Hawkins GB/SA Score Parameters
+[[File:First_side_chain.png|600px]]
-------------------------------------------------------------------------------------------
-SASA Score Parameters
+[[File:Sc_menu.png|600px]]
-------------------------------------------------------------------------------------------
-Amber Score Parameters
+You want to view the sidechains that have better overall grid scores.
-------------------------------------------------------------------------------------------
+On the View Dock menu, go to Column --> Show --> Grid_Score.
+You'll see that the Grid_Score column is columned. Let's sort the Grid_Score
+column in descending order(i.e. from greatest to least). To do this, click on the
+Grid_Score title, you'll notice that there's now an arrow head over the column.
+Keep clicking on the column until you see that the arrow head is pointing up:
-Simplex Minimization Parameters
+[[File:sort.png|600px]]
-------------------------------------------------------------------------------------------
-                                              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
+Now the best scoring molecule that was grown is at the top of the list and here's what it looks like:
-------------------------------------------------------------------------------------------
-                                                   atom_model [all] (all | united):
-                                                vdw_defn_file [vdw.defn] ():
-                                               flex_defn_file [flex.defn] ():
-                                              flex_drive_file [flex_drive.tbl] ():
-------------------------------------------------------------------------------------------
-Initializing De Novo Growth Routines...
+[[File:bg.png|600px]]
- Reading the scaffold library from fraglib_scaffold.mol2...Could not open fraglib_scaffold.mol2. Program will terminate.
-No such file or directory(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ cd ../../
-(base) [ehspector@milan2 Tutorials]$ cd ../
-(base) [ehspector@milan2 AMS_536]$ ls
-class_project  commands.txt  Notes.txt  Tutorials
-(base) [ehspector@milan2 AMS_536]$ vi Notes.txt
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in
-(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
-/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
-(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99
-ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99': No such file or directory
-(base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw
-ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw': No such file or directory
-(base) [ehspector@milan2 de_novo]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/
-(base) [ehspector@milan2 parameters]$ ls
-                         fraglib_linker.mol2         prot.table.ambcrg.sybH
-antechamber               fraglib_scaffold.mol2       sa_fraglib.dat
-chem.defn                 fraglib_sidechain.mol2      screen.in
-chemgrid                  fraglib_torenv.dat          screen.para
-chem_match.tbl            leap                        vdw_AMBER_parm94.defn
-flex.defn                 na.table.ambcrg             vdw_AMBER_parm94.dock3_7.defn
-flex_drive_mod.tbl        pains_table_2019_09_01.dat  vdw_AMBER_parm94.dock3_7_one_C_3.defn
-flex_drive.tbl            pains_table.dat             vdw_AMBER_parm96.defn
-flex_just_OH.defn         ph4.defn                    vdw_AMBER_parm99.defn
-flex_mod2.defn            prot.table.ambcrg.ambH      vdw_de_novo.defn
-flex_mod.defn             prot.table.ambcrg.pdb3H     vdw.parms.amb
-fraglib_ga_scaffold.mol2  prot.table.ambcrg.pdbH      vdw.parms.update.amb
-(base) [ehspector@milan2 parameters]$ class
-(base) [ehspector@milan2 AMS_536]$ cd ls
--bash: cd: ls: No such file or directory
-(base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/
-(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out
-(base) [ehspector@milan2 de_novo]$ vi Du.out
-(base) [ehspector@milan2 de_novo]$ cd ..
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore   de_novo
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 2w26/ga_calc/
-(base) [ehspector@milan2 ga_calc]$ ;s
--bash: syntax error near unexpected token `;'
-(base) [ehspector@milan2 ga_calc]$ ls
-w26_fraglib.in             2w26_fraglib_scored.mol2     lib.sh
-W26_fraglib_linker.mol2    2W26_fraglib_sidechain.mol2  py.sh
-w26_fraglib.out            2W26_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
-W26_fraglib_rigid.mol2     full_fraglib.dat
-W26_fraglib_scaffold.mol2  full_sorted_fraglib.dat
-(base) [ehspector@milan2 ga_calc]$ vi 2w26_fraglib.in
-(base) [ehspector@milan2 ga_calc]$ cd ..
-(base) [ehspector@milan2 2w26]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ mkdir ga_calc
-(base) [ehspector@milan2 1O86]$ cd ..
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/2w26_fraglib.in 1O86/ga_calc/1O86_fraglib.in
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/lib.sh 1O86/ga_calc/lib.sh
-(base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/py.sh 1O86/ga_calc/py.sh
-(base) [ehspector@milan2 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan2 Tutorials]$ cd 1O86/
-(base) [ehspector@milan2 1O86]$ ls
-_structure        003_gridbox    005_dock       007_virtualscreen  009_rescore   de_novo
-_surface_spheres  004_energymin  006_footprint  008_cartesian_min  commands.txt  ga_calc
-(base) [ehspector@milan2 1O86]$ cd ga_calc/
-(base) [ehspector@milan2 ga_calc]$ ls
-O86_fraglib.in  lib.sh  py.sh
-(base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.in
-(base) [ehspector@milan2 ga_calc]$ vi lib.sh
-(base) [ehspector@milan2 ga_calc]$ bash lib.sh
-(base) [ehspector@milan2 ga_calc]$ ls
-O86_fraglib.in           1O86_fraglib_rigid.mol2     1O86_fraglib_sidechain.mol2  py.sh
-O86_fraglib_linker.mol2  1O86_fraglib_scaffold.mol2  1O86_fraglib_torenv.dat
-O86_fraglib.out          1O86_fraglib_scored.mol2    lib.sh
-(base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.out
-(base) [ehspector@milan2 ga_calc]$ ls
-O86_fraglib.in           1O86_fraglib_rigid.mol2     1O86_fraglib_sidechain.mol2  py.sh
-O86_fraglib_linker.mol2  1O86_fraglib_scaffold.mol2  1O86_fraglib_torenv.dat
-O86_fraglib.out          1O86_fraglib_scored.mol2    lib.sh
-(base) [ehspector@milan2 ga_calc]$ vi py.sh
-(base) [ehspector@milan2 ga_calc]$ module list
-Currently Loaded Modulefiles:
-) slurm/seawulf3/21.08.8   3) gcc/13.2.0               5) gcc-stack
-) shared                   4) mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan2 ga_calc]$ module load python
-(base) [ehspector@milan2 ga_calc]$ bash py.sh
-(base) [ehspector@milan2 ga_calc]$ ls
-O86_fraglib.in             1O86_fraglib_scored.mol2     lib.sh
-O86_fraglib_linker.mol2    1O86_fraglib_sidechain.mol2  py.sh
-O86_fraglib.out            1O86_fraglib_torenv.dat      unique_full_sorted_fraglib.dat
-O86_fraglib_rigid.mol2     full_fraglib.dat
-O86_fraglib_scaffold.mol2  full_sorted_fraglib.dat
-(base) [ehspector@milan2 ga_calc]$ pwd
-/gpfs/home/ehspector/AMS_536/Tutorials/1O86/ga_calc
-(base) [ehspector@milan2 ga_calc]$ cd ../de_novo/
-(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out
-(base) [ehspector@milan2 de_novo]$ vi Du.out
-(base) [ehspector@milan2 de_novo]$ vi Du.in
-(base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
-Segmentation fault (core dumped)
-(base) [ehspector@milan2 de_novo]$ la
--bash: la: command not found
-(base) [ehspector@milan2 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
-(base) [ehspector@milan2 de_novo]$ vi Du.out
-(base) [ehspector@milan2 de_novo]$ vi 1O86_ligand_Du.mol2
-(base) [ehspector@milan2 de_novo]$ exit
-logout
-Connection to milan.seawulf.stonybrook.edu closed.
-(base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
-ehspector@milan.seawulf.stonybrook.edu's password:
-Duo two-factor login for ehspector
-Enter a passcode or select one of the following options:
+Load in the <code> 1O86_fixed_protein.pdb </code> and the <code> 1O86_ligand_nH_ncH.mol2 </code>.
+On Chimera, select Actions --> Ribbon --> hide.
+This will give a clear picture of the ligand having slight overlap with the grown ligand in the protein:
-. Duo Push to XXX-XXX-9204
+[[File:overlap.png|600px]]
-Passcode or option (1-1): 1
+Congratulations, you've successfully run a generic denovo calculation.
-Pushed a login request to your device...
-Success. Logging you in...
-Loading gcc-stack
-  Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
-(base) [ehspector@milan1 ~]$ class
-(base) [ehspector@milan1 AMS_536]$ cd Tutorials/
-(base) [ehspector@milan1 Tutorials]$ ls
-O86  2w26  5EEN
-(base) [ehspector@milan1 Tutorials]$ cd 1O86/de_novo/
-(base) [ehspector@milan1 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ vi Du.out
-(base) [ehspector@milan1 de_novo]$ vi Du.in
-(base) [ehspector@milan1 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
-Segmentation fault (core dumped)
-(base) [ehspector@milan1 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out  Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ vi Du.out
-(base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ vi Du.out
-(base) [ehspector@milan1 de_novo]$ vi 1O86_ligand_Du.mol2
-(base) [ehspector@milan1 de_novo]$ rm 1O86_ligand_Du.mol2
-(base) [ehspector@milan1 de_novo]$ ls
-Du.in  Du.out  Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ rm Du.out
-(base) [ehspector@milan1 de_novo]$ ls
-O86_ligand_Du.mol2  Du.in  Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
-(base) [ehspector@milan1 de_novo]$ ls
-O86_ligand_Du.mol2  Du.out                             Du.out.completed.denovo_build.mol2
-Du.in                Du.out.anchor_1.root_layer_1.mol2  Du.out.denovo_build.mol2
-(base) [ehspector@milan1 de_novo]$ vi Du.out
-(base) [ehspector@milan1 de_novo]$ vi Du.in
-conformer_search_type                                        denovo
-dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
-dn_fraglib_linker_file                                       /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_linker.mol2
-dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
-dn_user_specified_anchor                                     yes
-dn_fraglib_anchor_file                                       1O86_ligand_Du.mol2
-dn_torenv_table                                              ../ga_calc/unique_full_sorted_fraglib.dat
-dn_name_identifier                                           denovo
-dn_sampling_method                                           graph
-dn_graph_max_picks                                           30
-dn_graph_breadth                                             3
-dn_graph_depth                                               2
-dn_graph_temperature                                         100.0
-dn_pruning_conformer_score_cutoff                            100.0
-dn_pruning_conformer_score_scaling_factor                    2.0
-dn_pruning_clustering_cutoff                                 100.0
-dn_remove_duplicates                                         yes
-dn_max_duplicates_per_mol                                    0
-dn_write_pruned_duplicates                                   no
-dn_advanced_pruning                                          yes
-dn_prune_initial_sample                                      yes
-dn_sample_torsions                                           yes
-dn_prune_individual_torsions                                 yes
-dn_prune_combined_torsions                                   yes
-dn_random_root_selection                                     no
-dn_mol_wt_cutoff_type                                        soft
-dn_upper_constraint_mol_wt                                   1000
-dn_lower_constraint_mol_wt                                   0.0
-dn_mol_wt_std_dev                                            35.0
-dn_constraint_rot_bon                                        15
-dn_constraint_formal_charge                                  2.0
-dn_heur_unmatched_num                                        1
-dn_heur_matched_rmsd                                         2.0
-dn_unique_anchors                                            1
-dn_max_grow_layers                                           1
-dn_max_root_size                                             25
-dn_max_layer_size                                            25
-dn_max_current_aps                                           5
-dn_max_scaffolds_per_layer                                   1
-dn_max_successful_att_per_root                               50000
-dn_write_checkpoints                                         yes
-dn_write_prune_dump                                          yes
-dn_write_orients                                             no
-dn_write_growth_trees                                        no
-dn_output_prefix                                             Du.out
-use_internal_energy                                          yes
-internal_energy_rep_exp                                      12
-internal_energy_cutoff                                       100.0
-use_database_filter                                          no
-orient_ligand                                                no
-bump_filter                                                  no
-score_molecules                                              yes
-contact_score_primary                                        no
-grid_score_primary                                           yes
-grid_score_rep_rad_scale                                     1
-grid_score_vdw_scale                                         1
-grid_score_es_scale                                          1
-grid_lig_efficiency                                          no
-grid_score_grid_prefix                                       ../003_gridbox/grid
-minimize_ligand                                              yes
-minimize_anchor                                              yes
-minimize_flexible_growth                                     yes
-use_advanced_simplex_parameters                              no
-simplex_max_cycles                                           1
-simplex_score_converge                                       0.1
-simplex_cycle_converge                                       1.0
-simplex_trans_step                                           1.0
-simplex_rot_step                                             0.1
-simplex_tors_step                                            10.0
-simplex_anchor_max_iterations                                500
-simplex_grow_max_iterations                                  500
-simplex_grow_tors_premin_iterations                          0
-simplex_final_min                                            no
-simplex_random_seed                                          0
-simplex_restraint_min                                        no
-atom_model                                                   all
-vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
-flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
-flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl

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

Latest revision as of 13:41, 13 May 2025

Contents

DOCK Tutorial using PDB 1O86

000: Foundations

Chimera

Seawulf

SSH

Basic Unix Commands and Environment

SCP File Transfer

Directory setup

A Note on Troubleshooting

001: Structure Prep

Downloading the PDB

Protein Isolation

Inspecting the Protein

Protein Preparation

Isolating the Ligand

Preparing the Ligand

002: Spheres

Generate the Required Surface File

Selecting Spheres Localized on Binding Site

003: Grid/box

Generating the Box

Generating the Grid

004: Minimization

005: Rigid Docking

006: Flexible Docking

007: Footprint Scoring

008: 5K Virtual Screening

Input File

Slurm and Job Submission

Re-scoring Docked Molecules

Viewing VS Results in Chimera

009: Genetic Algorithm

Generating Fragments

Combining Fragment Libraries

Running the GA

Analysis

010: De Novo Design Example

De Novo Design

Selecting a Dummy Atom

Generating a Dummy Atom

Running The Denovo Calculation

Visualizing the Molecules in Chimera

Running a Generic De Novo Calculation

Selecting an Anchor

Running the Calculations

Visualizing The Results

Navigation menu

Search