2020 DOCK tutorial 2 with PDBID 2GQG

From Rizzo_Lab
Jump to: navigation, search

I. Introduction

DOCKING

DOCK, a commonly used computational tool used to sample a library of small molecules, ligands and attempts to successfully dock these within their target site, typically a rigid protein into their most energetically favorable positions. To accomplish this, first DOCK uses a global search of the entire protein to determine which locations will be the most energetically favorable, which will be the anchors. Following this, these ligands will take on a variety of different geometric poses to obtain the most conformationally favorable ligand positions. This software is commonly used to perform the hit to lead process in drug discovery to narrow down the drug possibilities from up to hundreds of millions to a few hundred. The drug discovery process then continues using this framework to further select and refine the potential drug candidates.


2GQG

This rigid protein is of the ABL Kinase Domain with the ligand being Dasatinib. This structure was identified using X-ray crystallography with a 2.4A resolution, lower resolutions are preferred.

Directories

For this part of the experiment, create an initial directory in your linux operating systems to work on your experiment

          mkdir 2GQG_Experiment

Following this change the directory to this directory

          cd 2GQG_Experiment

Use the mkdir command in your linux operating system to make all these directories to store your files for the experiment

          00.files
          01.dock_prep
          02.surface_spheres
          03.grid_box
          04.dock
          05.footprint
          06.virtual_screen
          07.virtual_screen_mpi
          08.cartesian_min
          09.rescore

II. Protein and Ligand Preparation

For the first step open up your chimera, go to file and fetch by ID to retrieve the PDB file 2GQG.

The Kinase is dimerized with another kinase to form 2 different chains so delete one of these chains. To produce the resulting image shown in Figure 1.

Check the structure

Read over the information for this protein-ligand complex to determine the charge and environment of the structure to make sure everything is correct. Make sure that there are no issues with the molecules, that aren't physically possible because otherwise they do not accurately represent the experimentally known.

Receptor Preparation

Open up the 2GQG.pdb file, Delete all non standard residues in the structures including the solvent molecules, water and the ligand. To do this task, go in chimera to select->residue->all-nonstd atoms. Following this delete these molecules.

Unique features specifically to this receptor, Delete the Phosphorous atom from this file because it isn't close to the docking site and this phosphorous atom is significantly difficult to parameterize. Also swap two of the residues in the protein structure, the PTR residue on residue 172 with TYR and the ARG residue on 164 with another ARG. To swap these residues, change these residue structures

Use this command line to switch the residue. This swaps the current 172 residue on chain a with tyr. Use this same command to swap the argine residues.

          swapaa tyr :172.a

Delete all the H's remaining on the receptor using the chimera database select->chemistry->elements->H. Then delete using the Actions->Atoms/bonds->delete command. Save this receptor as 2GQG_receptor_noH.mol2 using the command File->save mol2

Using the 2GQG_receptor_noH.mol2 add H's to the receptor with the command tools->structural editing->add H. Following this add amber charges to the molecule using the command tools-> structural editing-> add charge. The charge you should add are AM1BCC charges to the residues. Without these charges the coulomb's interaction wouldn't be calculated in the docking software.

Save the receptor as 2GQG_receptor_wH.mol2

Ligand Preparation

Open up the original PDB file in chimera, identify which nonstandard reside is the ligand using the select->residues->nonstd amino acid. Once the ligand has been selected use the inverted selected models select->invert(selected models) to select everything besides the ligand and delete these structures.

Add the hydrogens and AM1BCC charges to the ligand structure. Save this structure as 2GQG_ligand_wH.mol2

Add all these files into the 01.dock_prep directory

III. Generating Surface and Spheres

The purpose of this part is determine the anchor positions on the protein which is where the ligands will grow from.

DMS File Preparation

Open the 2GQG_receptor_noH.mol2 within Chimera, make sure to use the receptor file with no H.

First calculate the surface shape of the receptor using action-> surface -> show

Save this sphere file into a DMS file using the command Tools-> Structural Editing -> Write DMS and save as 2GQG_receptor_noH.dms

Generating Spheres

change directories into the 03.surface_spheres directory

      cd 03.surface_spheres

Create a new file titled INSPH using the vim command in linux, then type the following into the INSPH file

      vim INSPH

This file generates all the spheres that are capable of occupying the protein.

2GQG_receptor_noH.dms
R
X
0.0
4.0
1.4
2GQG_receptor_noH.sph

The first line specifies the surface file of the receptor. The R tells the program to generate external spheres, not internal ones; the X represents all points on the surface; 0.0 specifies the minimum distance between spheres and the surface - 0.0 avoids steric clashes; 4.0 and 1.4 are the maximum and minimum sphere radii. Once the INSPH file is ready, generate the spheres themselves using the following command:

sphgen -i INSPH -o OUTSPH

The sphgen program will calculate the spheres and write them to the file specified in INSPH, and print a description of the program running to OUTSPH.

Selecting Spheres

This will selectively choose the spheres in the sphere file previously made and choose the spheres less than 10.0 angstroms. The purpose of this part is to narrow the docking process by choosing only the places that are in the binding pocket of the ligand. If this search isn't performed the dock search would run docking simulations attempting to dock the ligand into unfavorable binding sites, both wasting computational resources and producing inaccurate results.

sphere_selector 2GQG_receptor_noH.sph ../01.dock_prep/2GQG_ligand_wH.mol2

The selected spheres will be written to the file selected_spheres.sph

IV. Box and Energy Grid

When docking small molecules to proteins, DOCK software uses a pre-generated energy grid to calculate the energy score between any given ligand pose and the static, rigid receptor. DOCK also often ignores any part of the receptor that is too far from the ligand binding site, to avoid excessive long-distance contacts and focus on local contacts near the binding site. This cutoff is created in the form of a box around the selected spheres.

Generating the Box

First, move to the appropriate directory for grid and box preparation:

cd ../03.grid_box

Similar to sphgen above, the showbox program uses an input file with paramaters. Create this file:

vim showbox.in

and fill it with these lines:

Y
8.0
../02.surface_spheres/selected_spheres.sph
1
2GQG.box.pdb

The Y tells the program to generate a box; 8.0 is how far out (in angstroms) the box edges should be from the spheres; the third line is the path to the selected sphere; the last line is the path for the box output as a pdb file. Run the showbox command with showbox.in as an input file:

showbox < showbox.in

This will generate the file 2GQG.box.pdb.

Grid Calculation

Next, we are going to use the program 'grid' to generate a grid. This program needs an input file. This file can either be empty or pre-filled with parameters; if using an empty file, the program will prompt the user for the value of each parameter.

Create the input file:

touch grid.in

Then run the program, with this file after the input flag:

grid -i grid.in

Answer the prompts with the following parameters, or fill the grid.in file in advance using vim:

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                        12
distance_dielectric                       yes
dielectric_factor                         4
bump_filter                               yes
bump_overlap                              0.75
receptor_file                             ../01.dock_prep/2GQG_receptor_wH.mol2
box_file                                  2GQG.box.pdb
vdw_definition_file                       /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
score_grid_prefix                         grid

The parameters generally have descriptive names. Essentially, this will generate an energy function grid with a potential at each point every 0.4 angstroms. The grid will have no contact score, an energy score using an all-atom force field with a 6-12 Lennard-Jones potential and a distance dielectric of 4. The last three lines specify the paths to the box defining the boundaries of the grid, the force field parameters, and the prefix for the output files.

If the program runs successfully, it will take a few minutes as it is a non-trivial calculation. The program will create three files: grid.bmp, grid.nrg, and gridinfo.out. Check the .out file to make sure the program was successful; make sure the overall charge is an integer and matches the charge of the original receptor file.

V. Single-Molecule Docking

To test the grid and other files prepared, the ligand from the crystal structure will be docked back into the receptor for pose reproduction.

Energy Minimization

First, energy minimization of the ligand is necessary, to make sure the ligand file used in docking is appropriate for the force field and will behave well. Move to the docking directory:

cd ../04.dock

From here, dock6 is the main program we are using. Similar to grid, this program can accept an input file full of parameters or an empty file filled based on answers to prompts on the command line. Create an input file for the minimization parameters:

touch min.in

Then run the DOCK program:

dock6 -i min.in

Answer the prompts or pre-fill the input file with the following parameters:

conformer_search_type                                        rigid                                          
use_internal_energy                                          yes                                            
internal_energy_rep_exp                                      12                                             
internal_energy_cutoff                                       100.0                                          
ligand_atom_file                                             ../1.dock_prep/2GQG_ligand_wH.mol2
limit_max_ligands                                            no                                             
skip_molecule                                                no                                             
read_mol_solvation                                           no                                             
calculate_rmsd                                               yes                                            
use_rmsd_reference_mol                                       yes                                            
rmsd_reference_filename                                      ../1.dock_prep/2GQG_ligand_wH.mol2
use_database_filter                                          no                                             
orient_ligand                                                no                                             
bump_filter                                                  no                                             
score_molecules                                              yes                                            
contact_score_primary                                        no                                             
contact_score_secondary                                      no                                             
grid_score_primary                                           yes                                            
grid_score_secondary                                         no                                             
grid_score_rep_rad_scale                                     1                                              
grid_score_vdw_scale                                         1                                              
grid_score_es_scale                                          1                                              
grid_score_grid_prefix                                       ../03.grid_box/grid                                         
multigrid_score_secondary                                    no                                             
dock3.5_score_secondary                                      no                                             
continuous_score_secondary                                   no                                             
footprint_similarity_score_secondary                         no                                             
pharmacophore_score_secondary                                no                                             
descriptor_score_secondary                                   no                                             
gbsa_zou_score_secondary                                     no                                             
gbsa_hawkins_score_secondary                                 no                                             
SASA_score_secondary                                         no                                             
amber_score_secondary                                        no                                             
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_random_seed                                          0                                              
simplex_restraint_min                                        yes                                            
simplex_coefficient_restraint                                10.0                                           
atom_model                                                   all                                            
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        2GQG_ligand_min                                   
write_orientations                                           no                                             
num_scored_conformers                                        1                                              
rank_ligands                                                 no

This program will calculate the energy-minimized ligand by relaxing internal degrees of freedom within the energy grid, and generate the new file 2GQG_ligand_min_scored.mol2. The RMSD between the original and new ligand will also be shown, it should be less than 2.0 angstroms. Visualize the differences in chimera.

Rigid Docking

Once energy minimization is completed, we can use the output of that energy minimization for the next step, which is docking. Create an input file for rigid docking

touch rigid.in

Run dock using the created input file.

dock6 -i rigid.in

Type in the following in the input file or answer the prompted questions manually

conformer_search_type                                        rigid
use_internal_energy                                          yes
ligand_atom_file                                             2GQG_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                                      2GQG_lig_min_scored.mol2
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2.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
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3.grid_box/grid
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        rigid.out
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

If rigid docking is successful, you will get an output file. (rigid.out_scored.mol2). Visualize the output file using Chimera

Open Chimera
File -> Open -> 2GQG_recptor_wH.mol2
File -> Open -> 2GQG_ligand_wH.mol2
Tools -> Surface/binding Analysis -> ViewDock -> Select the Rigid Dock output file. (rigid.out_scored.mol2)
In the loaded dialog box select Dock4,5 or 6

Once everything is loaded go to the ViewDock window, check the calculated properties to evaluate the output of rigid docking.

Column -> Show -> gridscore
Column -> Show -> HA_RMSDs
And some other useful properties such as vdw energy etc

RMSD <2A means the docking is reasonably successful.

Fixed Anchor Docking

only largest structured is fixed in Fixed anchor docking

Create an input file for fixed anchor docking.

touch fixed.in

Use the input file to perform fixed anchor docking

dock6 -i fixed.in

Copy these lines to the input file or to answer the prompted questions.

conformer_search_type                                        flex
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_conformer_score_cutoff                               100.0
pruning_conformer_score_scaling_factor                       1.0
use_clash_overlap                                            no
write_growth_tree                                            no
write_fragment_libraries                                     no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../1.dockprep/2GQG_ligand_wH.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       yes
rmsd_reference_filename                                      ../1.dockprep/2GQG_ligand_wH.mol2
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../2.grid_box/grid
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        2GQG_fad
write_orientations                                           no
num_scored_conformers                                        100
write_conformations                                          no
cluster_conformations                                        yes
cluster_rmsd_threshold                                       2.0
rank_ligands                                                 no

Output file will be generated. (2GQG_fad_scored.mol2) Visualize the result in Chimera following the same steps in rigid docking.

Flexible Docking

In flexible docking, all internal degree of freedom is sampled (most rigorous but computationally expensive).

Create a new input file for flexible docking.

touch flex.in

Use the created input file to perform flexible docking using DOCK6.

dock6 -i flex.in

Copy these lines to input file or answer prompted questions individually.

conformer_search_type                                        flex
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_conformer_score_cutoff                               100.0
pruning_conformer_score_scaling_factor                       1.0
use_clash_overlap                                            no
write_growth_tree                                            no
write_fragment_libraries                                     no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             2GQG.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                                      2GQG.lig.min_scored.mol2
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2.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
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3.grid_box/grid
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        flex.out
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no


output file (flex.out_scored.mol2) will be generated. Follow the same steps stated for rigid docking to examine the output. Flexible and Fixed Anchor Docking results are not good for this system.

VI. Virtual Screen

We will use the 5K molecules library (provided by instructor)

Move to new directory 7.virtual_screen. Copy the ligand library to the same directory.

Create a new input file for virtual screen.

touch virtual.in

Use the input file to perform virtual screen using DOCK6.

dock6 -i virtual.in

Copy following line to the input file

conformer_search_type                                        flex
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_conformer_score_cutoff                               100.0
pruning_conformer_score_scaling_factor                       1.0
use_clash_overlap                                            no
write_growth_tree                                            no
write_fragment_libraries                                     no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             5K_library.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no 
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2.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
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3.grid_box/grid
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no 
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        virtual.out
write_orientations                                           no 
num_scored_conformers                                        1
rank_ligands                                                 no

We will only use only 1 conformer for this as the library is very large, if we use more conformers, program will explode. Trial run on personal computer (crtl C to terminate if no problem is shown), but submit job to clusters using SLURM.

VI.Virtual Screen

The virtual screen method is a method to evaluate a large library of ligands and attempts to dock them into the same protein structure to form a protein-ligand complex. These compounds are then ranking by a variety of scoring methods such as Grid-Score, tanimoto, and pharmacophore.

The first step is to create an empty input file that is used to perform the virtual screen

touch -i virtual.in

To actually create the docking input file, use the dock6 command to input this command.

dock6 -i virtual.in

Input the following commands

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_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                                             ../VS_library_5K.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2.surface_spheres/2GQG_rec.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3.gridbox/Steves_grid/grid2
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        virtual_2GQG
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

This docking simulation runs will be performed for 25000 molecules and many simulations commonly use many more molecules so an mpi, message passing interface is used to work across multiple processors to speed up this process.

VII.Virtual Screen MPI

This mpi will allow you to run through the virtual screen across multiple processors

First create vim into your software

vim virtual.sh

Next input the following into the file

#!/bin/bash
#SBATCH --time=48:00:00
#SBATCH --nodes=4:ppn=28
#SBATCH --ntasks=24
#SBATCH --job-name=2GQG_VS_min
#SBATCH --output=2GQG_VS_min
#SBATCH -p rn-long
cd $SLURM_SUBMIT_DIR
dock6 -i virtual.in -o virtual.out

To submit the experiment to slurm submit the following command

qsub virtual.sh


VIII.Cartesian Minimization

Create empty input file for minimization

touch min.in

Use the dock6 program to generate the parameters for the input file

dock6 -i min.in

Input the following commands

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../6.virtual_screen/virtual_2GQG_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
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     yes
continuous_score_secondary                                   no
cont_score_rec_filename                                      ../1.dockprep/2gqg_chainA_rec_only_modified_5.mol2
cont_score_att_exp                                           6
cont_score_rep_exp                                           12
cont_score_rep_rad_scale                                     1
cont_score_use_dist_dep_dielectric                           yes
cont_score_dielectric                                        4.0
cont_score_vdw_scale                                         1
cont_score_es_scale                                          1
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        2GQG.virtualscreen.minimized
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

submit this minimization to the slurm docking program to minimize.

create the minimization submit script

touch min.sh
#!/bin/bash
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=24
#SBATCH --job-name=2GQG_VS_min
#SBATCH --output=2GQG_VS_min
#SBATCH -p rn-long
cd $SLURM_SUBMIT_DIR
dock6 -i min.in -o min.out

IX.Rescoring Docked Molecules

For this experiment, further evaluation of this program will be studied

touch rescore.in
dock6 -i rescore.in

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../6.virtual_screen/virtual_2GQG_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
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
footprint_similarity_score_primary                           no
footprint_similarity_score_secondary                         no
pharmacophore_score_primary                                  no
pharmacophore_score_secondary                                no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
descriptor_use_grid_score                                    no
descriptor_use_multigrid_score                               no
descriptor_use_continuous_score                              no
descriptor_use_footprint_similarity                          yes
descriptor_use_pharmacophore_score                           yes
descriptor_use_tanimoto                                      yes
descriptor_use_hungarian                                     yes
descriptor_use_volume_overlap                                yes
descriptor_fps_score_use_footprint_reference_mol2            yes
descriptor_fps_score_footprint_reference_mol2_filename       ../4.dock/2GQG_min_actual_scored.mol2
descriptor_fps_score_foot_compare_type                       Euclidean
descriptor_fps_score_normalize_foot                          no
descriptor_fps_score_foot_comp_all_residue                   yes
descriptor_fps_score_receptor_filename                       ../1.dockprep/2gqg_chainA_rec_only_modified_5.mol2
descriptor_fps_score_vdw_att_exp                             6
descriptor_fps_score_vdw_rep_exp                             12
descriptor_fps_score_vdw_rep_rad_scale                       1
descriptor_fps_score_use_distance_dependent_dielectric       yes
descriptor_fps_score_dielectric                              4.0
descriptor_fps_score_vdw_fp_scale                            1
descriptor_fps_score_es_fp_scale                             1
descriptor_fps_score_hb_fp_scale                             0
descriptor_fms_score_use_ref_mol2                            yes
descriptor_fms_score_ref_mol2_filename                       ../4.dock/2GQG_flex_scored.mol2
descriptor_fms_score_write_reference_pharmacophore_mol2      no
descriptor_fms_score_write_reference_pharmacophore_txt       no
descriptor_fms_score_write_candidate_pharmacophore           no
descriptor_fms_score_write_matched_pharmacophore             no
descriptor_fms_score_compare_type                            overlap
descriptor_fms_score_full_match                              yes
descriptor_fms_score_match_rate_weight                       5.0
descriptor_fms_score_match_dist_cutoff                       1.0
descriptor_fms_score_match_proj_cutoff                       0.7071
descriptor_fms_score_max_score                               20
descriptor_fingerprint_ref_filename                          ../4.dock/2GQG_flex_scored.mol2
descriptor_hms_score_ref_filename                            ../4.dock/2GQG_flex_scored.mol2
descriptor_hms_score_matching_coeff                          -5
descriptor_hms_score_rmsd_coeff                              1
descriptor_volume_score_reference_mol2_filename              ../4.dock/2GQG_flex_scored.mol2
descriptor_volume_score_overlap_compute_method               analytical
descriptor_weight_fps_score                                  1
descriptor_weight_pharmacophore_score                        1
descriptor_weight_fingerprint_tanimoto                       -1
descriptor_weight_hms_score                                  1
descriptor_weight_volume_overlap_score                       -1
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
chem_defn_file                                               /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/chem.defn
pharmacophore_defn_file                                      /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/ph4.defn
ligand_outfile_prefix                                        2GQG.descriptor.output
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

Other: dock preparation script

After the ligand and receptor .mol2 files and the surface .dms have been prepared in chimera, the other steps up to energy minimization can be completed with a bash script such as the following:

#!/bin/bash

# this script will generate spheres, select spheres, generate a box, calculate the grid, and minimize the ligand 

# necessary input files: 
# 1. clean receptor file with H and charge (.mol2)
# 2. clean receptor surface file with no H (.dms)
# 3. clean ligand file with H and charge (.mol2)

# usage: dockprep -r [receptor.mol2] -s [surface.dms] -l [ligand.mol2]

# assign input arguments to respective variables
while getopts r:s:l: option
do
	case "${option}"
		in
		r) RECEPTOR=${OPTARG};;
		s) SURFACE=${OPTARG};;
		l) LIGAND=${OPTARG};; 
 	esac
done

#create the INSPH file
INSPH='./INSPH'
SPHERES="rec_noH.sph"
if [ -s $INSPH ]
then
	if [ -r $INSPH ]
	then
		cp $INSPH "${INSPH}_old"
		rm $INSPH
	else
	echo "error: INPSH exists and does not have permission to read"
	fi
fi
touch $INSPH
echo "$SURFACE" > $INSPH
echo R >> $INSPH
echo X >> $INSPH
echo 0.0 >> $INSPH
echo 4.0 >> $INSPH
echo 0.4 >> $INSPH
echo $SPHERES >> $INSPH

#create the spheres using sphgen
sphgen -i INSPH -o OUTSPH 

#select spheres within 10.0 angstroms of the ligand and move the output into the 2.spheres directory
sphere_selector $SPHERES $LIGAND 10.0
SELECTEDSPH="./selected_spheres.sph" 

#create the showbox.in file
BOX="./rec.box.pdb"
BOXIN="./showbox.in"
touch $BOXIN
echo Y > $BOXIN
echo 8.0 >> $BOXIN
echo $SELECTEDSPH >> $BOXIN
echo 1 >> $BOXIN
echo $BOX >> $BOXIN 

showbox < $BOXIN 

#create the grid.in file and the grid files
echo -e "
compute_grids\t                             yes\n
grid_spacing\t                              0.4\n
output_molecule\t                           no\n
contact_score\t                             no\n
energy_score\t                              yes\n
energy_cutoff_distance\t                    9999\n
atom_model\t                                a\n
attractive_exponent\t                       6\n
repulsive_exponent\t                        12\n
distance_dielectric\t                       yes\n
dielectric_factor\t                        4\n
bump_filter\t                               yes\n
bump_overlap\t                              0.75\n
receptor_file\t                             ${RECEPTOR}\n
box_file\t                                  ${BOX}\n
vdw_definition_file\t                       /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn\n
score_grid_prefix\t                         grid\n
" > grid.in
grid -i grid.in -o gridinfo.out

#minimize the ligand
echo "conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             $LIGAND
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       yes    
rmsd_reference_filename                                      $LIGAND
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ./grid
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
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_random_seed                                          0
simplex_restraint_min                                        yes
simplex_coefficient_restraint                                10.0
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        lig.min
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no
" > min.in
dock6 -i min.in -o min.out