2023.05.08.6OIM_covalent - tbalius/teb_docking_test_sets GitHub Wiki
Covalent docking tutorial using KRAS in complex with Sotorasib/AMG 510 (PDB ID 6OIM)
Here we describe performing covalent docking with the following:
- DOCK 3 (DOCKovalent)
- DOCK 6 attach-and-grow algorithm (not released yet)
- DOCK 6 HDB covalent (not released yet)
Software requirements
- Python 2 environment with the following packages: Numpy
- Python 3 environment with the following packages: Numpy, RDKit
- AmberTools
- ChemAxon, Corina, and Amsol 7.1 for database generation.
- UCSF Chimera for visualization and running Dock Prep on the command line.
- DOCK 3.7 for preparing the receptor using blastermaster (Python 2 program) and for docking.
- DOCK 6.12 for database generation, calculating RMSD, and for docking with attach-and-grow (not released yet).
Organizing file directories
Directories for this tutorial:
6OIM_covalent_tutorial/
|-- dockprep/
|-- build_ligand_dock3/
|-- build_ligand_dock6/
|-- run_dock3/
|-- run_dock6/
+-- run_dock6_hdb/
Scripts on GitHub for this tutorial:
0001.processing.csh
0002.run_chimera_dockprep.csh
0002p5.fix_broken_h.csh
0003.run.antechamber.csh
0004.blastermaster.csh
0004.blastermaster_manualProt.csh
0005.convert_dock3_to_dock6.csh
0006.dock6_cov_sph.csh
setup.csh
calc_rmsd_dock3.csh
calc_rmsd_dock6.csh
mol2_python3.py*
mol_covalent_Si_to_Du_solv.py*
mol2_replace_sybyl_with_ele.py*
multimol2_removeH.py*
* available in teb_script_programs
Dock Prep
Prepare the system for docking in the dockprep directory.
Scripts are available here.
Download the Dock Prep scripts from GitHub by running the following wget commands:
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0001.processing.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0002.run_chimera_dockprep.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0002p5.fix_broken_h.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0003.run.antechamber.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0004.blastermaster.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0004.blastermaster_manualProt.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0005.convert_dock3_to_dock6.csh
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0006.dock6_cov_sph.csh
Copy and paste the code block into a C shell script and run the script.
>> csh download_scripts.csh
You will need to modify several of the scripts.
If there is a call to a script not available in this repository, it is most likely available in teb_scripts_programs.
Prepare the receptor and cofactors
To prepare the receptor and cofactor files, run the following scripts in order:
>> csh 0001.processing.csh
>> csh 0002.run_chimera_dockprep.csh
>> csh 0002p5.fix_broken_h.csh
>> csh 0003.run.antechamber.csh
The 0001.processing.csh script downloads the 6OIM.pdb file from the web and splits the file into receptor (with magnesium ion), ligand, and cofactor files called rec.pdb, lig.pdb, and cof.pdb, respectively. The 0002.run_chimera_dockprep.csh script calls Chimera's Dock Prep and AddH functions on the receptor and cofactor files. The 0002p5.fix_broken_h.csh script fixes a protonation error made by Chimera's AddH by replacing the name and coordinates of the incorrect hydrogen in the cofactor file with the name and coordinates of the correct hydrogen. The 0003.run.antechamber.csh script runs Amber's AnteChamber to calculate charges.
Generate spheres and grids
Use blastermaster to generate DOCK 3 spheres and grids, run the following scripts in order:
>> csh 0004.blastermaster.csh
>> csh 0004.blastermaster_manualProt.csh
- Note: you will need to wait for the blastermaster jobs to finish before proceeding
The 0004.blastermaster.csh script runs blastermaster on the receptor without the cofactor. The 0004.blastermaster_manualProt.csh script runs blastermaster on the receptor with the cofactor. Blastermaster is called with covalent flags.
Check the matching_spheres.sph file created by blastermaster in the blastermaster_cof/dockfiles directory, the last three lines should be formatted as follows:
9001 -4.51400 -4.02200 2.39800 1.000 1 0 0
9002 -5.43200 -4.54500 1.28800 1.000 1 0 0
9003 -6.34400 -3.26000 0.40900 1.000 1 0 0
Blastermaster generates grids for DOCK 3. To convert the grids to DOCK 6 readable grids, run the 0005.convert_dock3_to_dock6.csh script.
>> csh 0005.convert_dock3_to_dock6.csh
To generate covalent spheres for covalent docking with DOCK 6, run the 0005.dock6_cov_sph.csh script.
>> csh 0006.dock6_cov_sph.csh
This script greps for the atom lines of the gamma sulfur, beta carbon, and alpha carbon of cysteine 12 from rec.pdb, saves them to a PDB file called cov_sph.pdb, and then calls pdbtosph generate the cov_sph.sph sphere file.
Check the cov_sph.pdb file inside the created dock6_cov_spheres directory, it should be formatted as follows:
ATOM 93 SG CYS A 12 -6.344 -3.260 0.409 1.00 26.89 S
ATOM 92 CB CYS A 12 -5.432 -4.545 1.288 1.00 24.31 C
ATOM 89 CA CYS A 12 -4.514 -4.022 2.398 1.00 23.24 C
The DOCK 6 attach-and-grow covalent docking algorithm converts three atoms from the covalent cysteine sidechain into spheres for orienting: the alpha carbon, beta carbon, and gamma sulfur. The spheres must be in this specific order: 1) gamma 2) beta 3) alpha. This order is different from the covalent spheres file created by blastermaster used for covalent docking with DOCK 3.
To manually prepare covalent spheres for docking with DOCK 6, determine the gamma, beta, and alpha atoms of the covalent residue of interest, save the relevant atom lines to a pdb or mol2 file in the correct order, and convert the file to a sphere file using pdbtosph (distributed with DOCK 3) or mol2toSPH.py (available in teb_scripts_programs). This can also be applied to covalent residues other than cysteine (e.g. for serine use the gamma oxygen, beta carbon, and alpha carbon).
DOCK 3
Build ligand from SMILES
Database generation requires DOCK 6.12 and the following programs: ChemAxon, Corina, and Amsol 7.1.
Prepare the ligand database for covalent docking with DOCK 3 inside the build_ligand_dock3 directory.
Create a SMILES file called mov.smi containing the SMILES string of sotorasib.
O=C(N1CCN(C2=NC(N(c3c(C(C)C)nccc3C)c4nc(c5c(F)cccc5O)c(F)cc42)=O)[C@@H](C)C1)CC[SiH3] MOV
The SMILES has been modified for covalent docking by attaching a silicon atom where the molecule forms a covalent bond. This atom will be used to attach the ligand onto the receptor during docking.
RDKit can be used to process multiple SMILES by applying a reaction that appends the silicon atoms to your covalent warhead(s).
Sample DB2 generation scripts are distributed with DOCK 6.12. The sample DB2 generation pipeline requires the following programs: ChemAxon, Corina, and Amsol 7.1. ChemAxon's cxcalc is used for protonation, Corina is used to generate a 3d conformation of the ligand from SMILES, and Amsol 7.1 is used to calculate solvation free energies. DOCK 6 is used to generate multiple conformations of the ligand which are saved in a DB2 file. You will need to modify the scripts to run using the paths to your installed programs or to make program substitutions.
Run the ligand building script, the arguments passed are a SMILES file with your covalent ligand SMILES and a covalent flag.
>> csh ${dock6_path}/template_pipeline/hdb_lig_gen/generate/build_ligand_simple_with_dock6.csh mov.smi --covalent
- ${dock6_path} is a variable (placeholder) for the DOCK 6 installation path (e.g. /home/baliuste/zzz.github/dock6)
After the script finishes running, check that DB2 files were generated inside the db_build_working directory. The resulting DB2 files are called output_anchorX_scored.db2.gz.
>> ls db_build_working/MOV/MOV_*_db2/*.db2.gz
Run covalent docking with DOCK 3
Run DOCK in the run_dock3 directory.
Download the setup script to run covalent docking with DOCK 3.
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/setup.csh
This script creates two files: split_database_index and INDOCK. The split_database_index file contains the paths of the ligand database (.db2.gz) files prepared in the previous steps. The INDOCK file is an input file containing the parameters to run covalent docking with DOCK 3, and is created by copying and modifying the INDOCK file created by blastermaster. The script also creates a symbolic link to the dockfiles directory.
The created INDOCK file should be formatted as follows:
DOCK 3.7 parameter
#####################################################
# NOTE: split_database_index is reserved to specify a list of files
# defults for large scale docking.
ligand_atom_file split_database_index
#####################################################
# OUTPUT
output_file_prefix test.
#####################################################
# MATCHING
match_method 2
distance_tolerance 0.05
match_goal 1000
distance_step 0.05
distance_maximum 0.5
timeout 10.0
nodes_maximum 4
nodes_minimum 4
bump_maximum 1000.0
bump_rigid 1000.0
mol2_score_maximum 1000.0
#####################################################
# COLORING
chemical_matching no
case_sensitive no
#####################################################
# SEARCH MODE
atom_minimum 4
atom_maximum 25
number_save 1
number_write 1
flush_int 100
#molecules_maximum 100000
check_clashes no
do_premax no
do_clusters no
#####################################################
# SCORING
ligand_desolvation volume
#vdw_maximum 1.0e10
ligand_desolv_scale 1.0
electrostatic_scale 1.0
vdw_scale 1.0
internal_scale 0.0
per_atom_scores no
#####################################################
# DOCKovalent
dockovalent yes
bond_len 1.8
bond_ang1 109.5
bond_ang2 109.5
len_range 0.0
len_step 0.1
ang1_range 10.0
ang2_range 10.0
ang1_step 2.5
ang2_step 2.5
#####################################################
# MINIMIZATION
minimize no
sim_itmax 500
sim_trnstep 0.2
sim_rotstep 5.0
sim_need_to_restart 1.0
sim_cnvrge 0.1
min_cut 1.0e15
iseed 777
#####################################################
# INPUT FILES / THINGS THAT CHANGE
receptor_sphere_file ./dockfiles/matching_spheres.sph
vdw_parameter_file ./dockfiles/vdw.parms.amb.mindock
delphi_nsize 99
flexible_receptor no
total_receptors 1
############## grids/data for one receptor
rec_number 1
rec_group 1
rec_group_option 1
solvmap_file ./dockfiles/ligand.desolv.heavy
hydrogen_solvmap_file ./dockfiles/ligand.desolv.hydrogen
delphi_file ./dockfiles/trim.electrostatics.phi
chemgrid_file ./dockfiles/vdw.vdw
bumpmap_file ./dockfiles/vdw.bmp
############## end of INDOCK
Run DOCK 3.
>> ${DOCKBASE}/bin/dock64
- ${DOCKBASE} is a variable (placeholder) for the DOCK 3 installation path (e.g. /home/baliuste/zzz.github/DOCK)
Once DOCK 3 finishes running, unzip the output mol2 file.
>> gunzip test.mol2.gz
The unzipped mol2 file can be visualized in Chimera using ViewDock.
Calculate RMSD
Download the following scripts from the teb_scripts_programs repository:
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/mol2_python3.py
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/mol2_replace_sybyl_with_ele.py
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/multimol2_removeH.py
The mol2_replace_sybyl_with_ele.py script takes a mol2 file as input and outputs a mol2 file with the sybyl atom types replaced with the element symbol. The multimol2_removeH.py removes the hydrogens from a mol2 file. The mol2_python.py script is required to run the other two scripts.
Download the calc_rmsd_dock3.csh script from this repository.
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/calc_rmsd_dock3.csh
This script creates the files needed for calculating RMSD before calling DOCK 6 to calculate RMSD. First, the lig.pdb file created during Dock Prep is converted into a Mol2 file called ref.mol2 using Chimera. Then the mol2_replace_sybyl_with_ele.py script is run on the reference Mol2 file, ref.mol2, and the output file created by DOCK, test.mol2. The multimol2_removeH.py script is run to remove hydrogens from test.mol2. Finally, a DOCK 6 input file called rmsd.in is created and DOCK 6 is run to calculate RMSD.
Modify the script by changing the chimera path, the parameter file paths in the rmsd.in file, and the path to call DOCK 6 to your Chimera and DOCK 6 installation path.
Run the script.
>> csh calc_rmsd_dock3.csh
The rmsd_output_scored.mol2 file contains the poses with the corresponding RMSD values in the header. The Hungarian (symmetry-corrected) heavy-atom RMSD is labeled as HA_RMSDh.
########## HA_RMSDh: 10.216
########## HA_RMSDh: 5.045
DOCK 6
Build ligand from SMILES
Prepare the ligand database for covalent docking with DOCK 6 attach-and-grow inside the build_ligand_dock6 directory.
Create a SMILES file called mov.smi containing the SMILES string of sotorasib.
O=C(N1CCN(C2=NC(N(c3c(C(C)C)nccc3C)c4nc(c5c(F)cccc5O)c(F)cc42)=O)[C@@H](C)C1)CC[SiH2][SiH3] MOV
The SMILES has been modified for covalent docking by attaching two silicon atoms where the molecule forms a covalent bond. For covalent docking with DOCK 6 attach-and-grow, the ligand is prepared with two dummy atoms instead of one. The two dummy atoms are aligned to the gamma sulfur and beta carbon atoms of the covalent cysteine residue during docking.
RDKit can be used to process multiple SMILES by applying a reaction that appends the silicon atoms to your covalent warhead(s).
Run the ligand building script, the arguments passed are a SMILES file with your covalent ligand SMILES and a covalent flag.
>> csh ${dock6_path}/template_pipeline/hdb_lig_gen/generate/build_ligand_simple_with_dock6.csh mov.smi --covalent
Download a script from the teb_scripts_programs repository:
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/mol_covalent_Si_to_Du_solv.py
This script converts silicon atoms to dummy atoms and appends the solvation parameters.
Paste the following code into a C shell script and run the script:
foreach mol2 (`ls db_build_working/*/*_output.mol2`)
python mol_covalent_Si_to_Du_solv.py $mol2 ${mol2:r}.solv temp_Du 103 >> log
cat temp_Du.mol2 >> ligand_cov.mol2
rm temp_Du.mol2
end
>> csh mk_mol2_cov.csh
This will loop over each Mol2 file created by the ligand building script and run the mol_covalent_Si_to_Du_solv.py script, the output for each Mol2 file is appended to a file called ligand_cov.mol2. The ligand_cov.mol2 file will be used as input for covalent docking with DOCK 6.
Run covalent docking with DOCK 6 attach-and-grow
Create an input file for DOCK 6 called covalent.in and format it as follows:
conformer_search_type covalent
pruning_use_clustering yes
pruning_max_orients 1000
pruning_clustering_cutoff 100
covalent_bondlength 1.7:0.1:1.91
covalent_bondlength2 1.7:0.1:1.91
covalent_angle 103.0:1.0:105.0
covalent_dihedral_step 10.0
pruning_conformer_score_cutoff 1000.0
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 ../build_ligand_dock6/ligand_cov.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation yes
calculate_rmsd yes
use_rmsd_reference_mol no
use_database_filter no
orient_ligand yes
automated_matching yes
receptor_site_file ../dockprep/dock6_cov_spheres/cov_sph.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 no
gist_score_primary no
multigrid_score_primary no
dock3.5_score_primary yes
dock3.5_vdw_score yes
dock3.5_grd_prefix ../dockprep/blastermaster_cof/dock6files/chem52
dock3.5_electrostatic_score yes
dock3.5_ligand_desolvation_score volume
dock3.5_solvent_occlusion_file ../dockprep/blastermaster_cof/dock6files/ligand.desolv.heavy
dock3.5_redistribute_positive_desolvation no
dock3.5_hydrogen_desolvation_grid yes
dock3.5_hydrogen_solvent_occlusion_file ../dockprep/blastermaster_cof/dock6files/ligand.desolv.hydrogen
dock3.5_receptor_desolvation_score no
dock3.5_write_atomic_energy_contrib no
dock3.5_score_vdw_scale 1
dock3.5_score_es_scale 1
minimize_ligand yes
minimize_anchor no
minimize_flexible_growth yes
use_advanced_simplex_parameters no
minimize_flexible_growth_ramp 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_grow_max_iterations 0
simplex_grow_tors_premin_iterations 500
simplex_final_min no
simplex_random_seed 0
simplex_restraint_min no
atom_model all
vdw_defn_file ${dock6_path}/parameters/vdw_AMBER_parm94.dock3_7.defn
flex_defn_file ${dock6_path}/parameters/flex.defn
flex_drive_file ${dock6_path}/parameters/flex_drive.tbl
ligand_outfile_prefix covalent.out
write_mol_solvation no
write_orientations no
num_scored_conformers 10
write_conformations no
cluster_conformations yes
cluster_rmsd_threshold 0.5
score_threshold 100.0
rank_ligands no
Replace ${dock6_path} in the parameter file lines with the DOCK 6 installation path.
The conformer_search_type input parameter is set to covalent, and four parameters to sample the covalent bond environment are introduced: covalent_bondlength, covalent_bondlength2, covalent_angle, and covalent_dihedral_step.
Here is a diagram of the covalent bond environment and values being sampled:
The covalent_bondlength, covalent_bondlength2, and covalent_angle parameters can given a single value or multiple values to iterate over using the form start:step:stop. In the example parameter file given above, the covalent_bondlength and covalent_bondlength2 parameter is set to 1.7:0.1:1.91, so bond lengths of 1.7, 1.8, and 1.9 will be sampled during docking for the two bonds. The covalent_angle parameter is set to 103.0:1.0:105.0, so covalent angles of 103.0, 104.0, and 105.0 will be sampled during docking. In total, the molecule will be docked in 27 different covalent bond environments. At the time this tutorial was written (November 2023), this docking took ~14 minutes (~833 seconds); when docking with a single bond environment, the docking took ~27 seconds.
Run DOCK 6.
>> ${dock6_path}/bin/dock6 -i covalent.in -o covalent.out -v
The covalent.out_scored.mol2 file can be visualized in Chimera using ViewDock.
The output Mol2 file is written with the dummy atoms still attached to the ligand. The two dummy atoms should overlap with the gamma sulfur and beta carbon of cysteine 12.
Calculate RMSD
Download the following scripts from the teb_scripts_programs repository:
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/mol2_python3.py
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/mol2_replace_sybyl_with_ele.py
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/multimol2_removeH.py
The mol2_replace_sybyl_with_ele.py script takes a mol2 file as input and outputs a mol2 file with the sybyl atom types replaced with the element symbol. The multimol2_removeH.py removes the hydrogens from a mol2 file. The mol2_python.py script is required to run the other two scripts. These are the same scripts used to prepare Mol2 files for RMSD calculation for covalent docking with DOCK 3.
Download the calc_rmsd_dock6.csh script from this repository.
wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/calc_rmsd_dock6.csh
This script creates the files needed for calculating RMSD before calling DOCK 6 to calculate RMSD. First, the lig.pdb file created during Dock Prep is converted into a Mol2 file called ref.mol2 using Chimera. The covalent.out_scored.mol2 is opened in Chimera and the dummy atoms are deleted. Then the mol2_replace_sybyl_with_ele.py script is run on the reference Mol2 file, ref.mol2, and the output file created by DOCK, covalent.out_scored.mol2. The multimol2_removeH.py script is run to remove hydrogens. Finally, a DOCK 6 input file called rmsd.in is created and DOCK 6 is run to calculate RMSD.
Modify the script by changing the chimera path, the parameter file paths in the rmsd.in file, and the path to call DOCK 6 to your Chimera and DOCK 6 installation paths.
Run the script.
>> csh calc_rmsd_dock6.csh
The rmsd_output_scored.mol2 file contains the poses with the corresponding RMSD values in the header. The Hungarian (symmetry-corrected) heavy-atom RMSD is labeled as HA_RMSDh.
########## HA_RMSDh: 0.749
########## HA_RMSDh: 1.275
########## HA_RMSDh: 0.696
The values for the bond environment from the crystal structure (PDB ID 6OIM) are d1 = 1.804331 Å, d2 = 1.805427 Å, and θ = 116.120121°. Even though we do not sample the exact bond angle, DOCK can still reproduce the crystallographic ligand pose.
Process SMILES with RDKit
We use RDKit's rdkit.Chem.rdChemReactions module to process multiple SMILES.
Download a script from the teb_scripts_programs repository:
wget https://raw.githubusercontent.com/tbalius/teb_scripts_programs/tree/master/zzz.scripts/simple_reaction_file.py
This script will apply a SMARTS reaction to each of your SMILES.
Sotorasib is used as an example:
O=C(N1CCN(C2=NC(N(c3c(C(C)C)nccc3C)c4nc(c5c(F)cccc5O)c(F)cc42)=O)[C@@H](C)C1)C=C MOV
Sotorasib has an acrylamide covalent warhead.
To append one silicon atom:
>> python simple_reaction_file.py "[SiH3:1].[C:2]=[C:3][C:4]=[O:5]>>[SiH3:1][C:2][C:3][C:4]=[O:5]" "[SiH3]" mov.smi mov_si.smi
To append two silicon atoms:
>> python simple_reaction_file.py "[SiH3:1][SiH2:2].[C:3]=[C:4][C:5]=[O:6]>>[SiH3:1][SiH2:2][C:3][C:4][C:5]=[O:6]" "[SiH2][SiH3]" mov.smi mov_si.smi
Change the reaction to target different covalent warheads. For vinyl sulfonamides:
>> python simple_reaction_file.py "[SiH3:1][SiH2:2].[C:3]=[C:4][S:5](=[O:6])=[O:7]>>[SiH3:1][SiH2:2][C:3][C:4][S:5](=[O:6])=[O:7]" "[SiH2][SiH3]" input.smi output.smi
Run covalent docking with DOCK 6 HDB covalent
We can also dock covalent DB2 files using DOCK 6 HDB covalent.
To prepare the ligand database, see the DOCK 3 section.
Copy or regenerate the split_database_index file used for DOCK 3.
../build_ligand_dock3/db_build_working/MOV/MOV_0_db2/output_anchor1_scored.db2.gz
../build_ligand_dock3/db_build_working/MOV/MOV_1_db2/output_anchor1_scored.db2.gz
Create an input file for DOCK 6 called covalent.in and format it as follows:
conformer_search_type HDB_covalent
num_per_search 10
skip_broken no
hdb_db2_input_file split_database_index
hdb_db2_search_score_threshold 1000.0
hdb_db2_search_covalent_bondlength1 1.8
hdb_db2_search_covalent_bondlength2 1.8
hdb_db2_search_covalent_bondlength3 1.8
hdb_db2_search_covalent_angle1 100.0
hdb_db2_search_covalent_angle2 100.0
hdb_db2_search_covalent_angle3 100.0
hdb_db2_search_covalent_dihederal_step1 10.0
hdb_db2_search_covalent_dihederal_step2 10.0
hdb_write_dummy_mol2 yes
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 ../dockprep/dock6_cov_spheres/cov_sph.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 no
gist_score_primary no
DistJoin_score_primary no
multigrid_score_primary no
dock3.5_score_primary yes
dock3.5_vdw_score yes
dock3.5_grd_prefix ../dockprep/blastermaster_cof/dock6files/chem52
dock3.5_electrostatic_score yes
dock3.5_ligand_desolvation_score volume
dock3.5_solvent_occlusion_file ../dockprep/blastermaster_cof/dock6files/ligand.desolv.heavy
dock3.5_redistribute_positive_desolvation no
dock3.5_hydrogen_desolvation_grid yes
dock3.5_hydrogen_solvent_occlusion_file ../dockprep/blastermaster_cof/dock6files/ligand.desolv.hydrogen
dock3.5_receptor_desolvation_score no
dock3.5_write_atomic_energy_contrib no
dock3.5_score_vdw_scale 1
dock3.5_score_es_scale 1
minimize_ligand no
simplex_final_min no
atom_model all
vdw_defn_file ${dock6_path}/parameters/vdw_AMBER_parm94.dock3_7.defn
flex_defn_file ${dock6_path}/parameters/flex.defn
flex_drive_file ${dock6_path}/parameters/flex_drive.tbl
ligand_outfile_prefix covalent.out
write_mol_solvation no
write_orientations no
num_scored_conformers 10
write_conformations no
cluster_conformations yes
cluster_rmsd_threshold 0.5
score_threshold 100.0
rank_ligands no
Run DOCK 6.
>> ${dock6_path}/bin/dock6 -i covalent.in -o covalent.out -v
The output Mol2 is written with one dummy atom attached to the ligand. Setting hdb_write_dummy_mol2 to no will tell DOCK to not write out the dummy atom in the output, which can be helpful for calculating RMSD.
The calc_rmsd_dock6.csh script used to calculate RMSD for attach-and-grow can be also used for HDB covalent.