macrocycle_docking.py Command Help
Command: $SCHRODINGER/run -FROM psp macrocycle_docking.py
usage: macrocycle_docking.py [-h] -target_ligand TARGET_LIGAND -receptor
RECEPTOR [-n_output_poses N_OUTPUT_POSES]
[-run_ffbuilder] [-long_help]
(-template_ligand TEMPLATE_LIGAND | -template_ligand_asl TEMPLATE_LIGAND_ASL | -binding_site_asl BINDING_SITE_ASL | -binding_site_center X Y Z | -grid GRID)
[-forcefield FORCEFIELD]
[-target_nconf TARGET_NCONF]
[-conformers_mae CONFORMERS_MAE]
[-shape_constraint_mae SHAPE_CONSTRAINT_MAE]
[-core_constraint_mae CORE_CONSTRAINT_MAE]
[-core_definition {all,allheavy,mcssmarts,smarts}]
[-core_smarts CORE_SMARTS]
[-core_pos_max_rmsd CORE_POS_MAX_RMSD] [-map MAP]
[-peptide]
[-prime_mcs_ene_z_cutoff PRIME_MCS_ENE_Z_CUTOFF]
[-glide_gscore_z_cutoff GLIDE_GSCORE_Z_CUTOFF]
[-glide_denscore_z_cutoff GLIDE_DENSCORE_Z_CUTOFF]
[-glide_out_poses_per_conf GLIDE_OUT_POSES_PER_CONF]
[-jobname JOBNAME] [-NJOBS NJOBS]
[-RETRIES RETRIES] [-v] [-HOST <hostname>]
[-WAIT] [-D] [-NOJOBID] [-NOLAUNCH]
Script for docking macrocycles with Prime macrocycle sampling and Glide docking.
options:
-h, --help show this help message and exit
-target_ligand TARGET_LIGAND
Target ligand to dock. Should be an MAE file.
-receptor RECEPTOR Receptor mae file (mae or maegz)
-n_output_poses N_OUTPUT_POSES
Number of final per-ligand poses returned to the top-level run folder; default = 10
-run_ffbuilder Create a customized force field for the torsions present in the -target_ligand file. If an OPLS_DIR is specified and torsions are missing from the directory, OPLS_DIR will be modified to include the missing parameters.
-long_help Print exhaustive help message.
-v show program's version number and exit
Grid Generation Options:
-template_ligand TEMPLATE_LIGAND
Template ligand file (mae or maegz). Used to define the center of a Glide docking grid.
-template_ligand_asl TEMPLATE_LIGAND_ASL
ASL defining a template ligand in the '-receptor' structure file. Used to define the center of a Glide docking grid. Atoms matching the ASL are removed prior to docking.
-binding_site_asl BINDING_SITE_ASL
ASL defining the binding site in the '-receptor' structure file. The centroid of the matching atoms is used to define the center of a Glide docking grid.
-binding_site_center X Y Z
X, Y and Z coordinates of the center of the Glide docking grid, separated by spaces, e.g. -binding_site_center 1.0 2.0 3.0
-grid GRID Use a custom Glide grid for docking and skip grid generation.
Docking Options:
-forcefield FORCEFIELD
Forcefield to use for calculations.
-target_nconf TARGET_NCONF
Target number of conformers to generate during the PrimeMCS sampling stage; default = 1000
-conformers_mae CONFORMERS_MAE
Manually specify ring conformers to use during the Glide docking stage and skip the PrimeMCS sampling stage.
-shape_constraint_mae SHAPE_CONSTRAINT_MAE
Reference ligand to generate shape constraints for the docking jobs.
-core_constraint_mae CORE_CONSTRAINT_MAE
Reference ligand to a generate core constraints for the docking jobs; cores are defined by the maximum common substructure between the reference structure and the target ligand.
-core_definition {all,allheavy,mcssmarts,smarts}
Method for defining the core for core constraints:
- all: All atoms in the reference structure.
- allheavy: All non-hydrogen atoms in the reference structure
- mcssmarts (default): The maximum common substructure between the reference structure and the target ligand, defined as a SMARTS string.
- smarts: A custom SMARTS string defining the core; use with -core_smarts to specify the SMARTS string.
-core_smarts CORE_SMARTS
Custom SMARTS string to define the core for core constraints.
-core_pos_max_rmsd CORE_POS_MAX_RMSD
Maximum RMSD of the core atom positions; default = None
-map MAP Experimental cryo-EM density file used for docking; supported extensions include .ccp4, .mrc, and .map.
-peptide Generate a peptide docking grid.
-prime_mcs_ene_z_cutoff PRIME_MCS_ENE_Z_CUTOFF
Energy-based z-score cutoff for structures generated during the PrimeMCS sampling stage; default = -0.25
-glide_gscore_z_cutoff GLIDE_GSCORE_Z_CUTOFF
Glide score-based z-score cutoff for structures generated during the Glide docking stage; default = -0.25
-glide_denscore_z_cutoff GLIDE_DENSCORE_Z_CUTOFF
Glide density score-based z-score cutoff for structures generated during the Glide docking stage; default = -0.25
-glide_out_poses_per_conf GLIDE_OUT_POSES_PER_CONF
Number of poses to return from each Glide docking sub-job; increasing this may increase docking accuracy at the expense of compute time; default = 1
Job Control Options:
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Set the base name of outputs
Standard Options:
-NJOBS NJOBS Divide the overall job into NJOBS subjobs.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried RETRIES times.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-D, -DEBUG Show details of Job Control operation.
-NOJOBID Run the job directly, without Job Control layer.
Standard Options:
-NOLAUNCH Set up subjob inputs, but don't run the jobs.