covalent_docking Command Help
Command: $SCHRODINGER/covalent_docking
usage:
$SCHRODINGER/covalent_docking [<options>] <jobName>.inp
OR
$SCHRODINGER/covalent_docking [<options>] <rec_file (mae format)>
<lig_file (mae format)>
<attachment_residue (ie A:1)>
<-rxn_type (rxn)>
positional arguments:
rec_file Input receptor structure (maestro format)
lig_file Input ligand structures (maestro format)
attachment_residue Attachment residue on the receptor in the format
<chain>:<residuenumber>, ie A:2, :3, A:21A
options:
-h, --help show this help message and exit
-v show program's version number and exit
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Set the base name of outputs
Covalent Docking Chemistry:
-mode {leadopt,enrichment,score,attach}
leadopt: (~1-3 hours/compound); enrichment:
(~10min/compound); score: create covalent complex to
test reaction definition -- input ligand position must
be reasonable; attach: ( 20s/compound ) Attach the
ligand and receptor with no scoring
-rxn_type {Michael Addition,Nucleophilic Addition to a Double Bond,Nucleophilic Addition to a Triple Bond,Nucleophilic Substitution,Nucleophilic Substitution of a Carbamate,Boronic Acid Addition,Epoxide Opening,Imine Condensation,Phosphonate Addition,Beta Lactam Addition,Conjugate Addition to Alkene (nitrile activated),Conjugate Addition to Alkyne (carbonyl activated),Conjugate Addition to Alkyne (aryl activated),Disulfide Formation,Ion Pair to Covalent Bond: Lig(-1)/Rec(+1),Ion Pair to Covalent Bond: Lig(+1)/Rec(-1)}, -reaction_type {Michael Addition,Nucleophilic Addition to a Double Bond,Nucleophilic Addition to a Triple Bond,Nucleophilic Substitution,Nucleophilic Substitution of a Carbamate,Boronic Acid Addition,Epoxide Opening,Imine Condensation,Phosphonate Addition,Beta Lactam Addition,Conjugate Addition to Alkene (nitrile activated),Conjugate Addition to Alkyne (carbonyl activated),Conjugate Addition to Alkyne (aryl activated),Disulfide Formation,Ion Pair to Covalent Bond: Lig(-1)/Rec(+1),Ion Pair to Covalent Bond: Lig(+1)/Rec(-1)}
Choose a reaction type from the above supported names.
-print_named_reactions
Print out the named reactions in cdock format then
exit.
-leaving_group LEAVING_GROUP
Leaving group (for Nucleophilic Substitution if
leaving group is not F,Br,Cl,I)
-ligand_pdb_atom_name PDB_ATOM_NAME
Provide the pdb atom name of the ligand atom to be
used for attachment if more than one atom matches the
ligand SMARTS pattern
-reaction_name REACTION_NAME
Custom reaction name (optional). If not defined, a
default "Custom", or in the case of a reaction file,
the file name will be used.
-custom_chemistry CUSTOM_CHEMISTRY
Pass in a custom chemistry to perform using the syntax
described in the Schrodinger knowledge base. Note that
-ligand_smarts_pattern and -receptor_smarts_pattern
are required.
-ligand_smarts_pattern LIGAND_SMARTS_PATTERN
SMARTS pattern and position on the ligand for
attachment. Should be in the form <position (start
from 1)>,<SMARTS_PATTERN> ie 1,[C;r3][O;r3][C;r3]
-receptor_smarts_pattern RECEPTOR_SMARTS_PATTERN
SMARTS pattern and position on the receptor for
attachment. Should be in the form <position (start
from 1)>,<SMARTS_PATTERN> ie 1,[C;r3][O;r3][C;r3]
-reaction_file REACTION_FILE
Use a pre-made reaction_file object for your specific
reaction.
-multi_reactions MULTI_REACTIONS, -multiple_reactions MULTI_REACTIONS
Define multiple reactions. Each reaction can be
defined with a reaction file or a supported reaction
type name.
Initial Docking:
-grid_option GRID_OPTIONS
Add a keyword-value pair to pass to initial Glide Grid
Generation stage in the format <keyword>=<value>. See
the "Running Glide From the Command Line" chapter in
the Glide User Manual for a description of available
options.
-grid_file GRID_FILE Pass in a grid file from a previous Covalent docking
job This grid file must be created from a previous
covalent docking job with the same receptor, the same
reactive residue and the same constraints as this one
-sample_dock_option SAMPLE_DOCK_OPTIONS
Add a keyword-value pair to pass to initial Glide
Ligand Docking stage in the format <keyword>=<value>.
See the "Running Glide From the Command Line" chapter
in the Glide User Manual for a description of
available options.
-cons_file CONS_FILE Use a file to define regular Glide constraints:
positional, hydrogen bond, and torsional. The
constraints should be the same format as in a Glide
input file.
-dist_constraint DIST_CONSTRAINT
Distance to use for constraint to attachment CB in the
Glide Docking stage
-reference_ligand REFERENCE_LIGAND
A mae-format file containg a similar ligand to the
desired ligand in a known active conformation (it
should be in the same frame of reference as the
receptor). Only the ligand should be included in this
file
-core_constraint_smarts CORE_CONSTRAINT_SMARTS
Use core constraints to the reference ligand using
this SMARTS pattern to define the core
-core_pos_max_rmsd CORE_POS_MAX_RMSD
Maximum allowed RMSD between the core of the reference
ligand and each docked ligand
-initial_sampling {standard,skip}
Sampling protocol to use on isolated ligand before
docking.standard: default for leadopt docking mode.
Use macromodel to sample poses before running. skip:
default for screening docking mode. Do not sample
ligand poses before docking.
-ncluster_init NCLUSTER_INIT
Maximum number of covalently bound poses per ligand to
generate (default - no Clustering)
Refining:
-init_gscore_cutoff INIT_GSCORE_CUTOFF
Cutoff used to select Glide poses for covalent bond
formation and further refinement (default 2.5)
-max_init_poses MAX_INIT_POSES
Maximum number of Glide poses to keep for covalent
bond formation and further refinement (default 200)
-min_bond_dist MIN_BOND_DIST
Discard any poses where the length of the covalent
bond formed between the ligand the protein is more
than this before refinement
-rotamer_sampling ROTAMER_SAMPLING
Reduce rotamer library sampling of attachment residue
1 is default, 2 is half the sampling, 3 is a third
-ncluster NCLUSTER Maximum number of covalently bound poses per ligand to
score (default Auto)
-nposes NPOSES Maximum number of covalently bound poses per ligand
reaction sites to output (default is all unique
poses).Ligands with two possible reaction sites will
return twice as many poses as ligands with only a
single reaction site.
-output_top OUTPUT_TOP
Report this number of top scoring ligands. Note that
when combined with -nposes the total number of poses
generated will be up to this values multiplied by the
maximum number of poses produced. By default poses for
all ligands will be generated if possible.
-min_option MIN_OPTIONS
Add a keyword-value pair to pass to Prime optimization
stage in the format <keyword>=<value>. See the
"Command Syntax" chapter in the Prime User Manual for
a description of available options.
-min_radius MIN_RADIUS
Radius around the ligand and attachment residue to
optimize with Prime. By default no receptor atoms are
optimized
-score_dock_option SCORE_DOCK_OPTIONS
Add a keyword-value pair to pass to final Glide Ligand
Docking stage in the format <keyword>=<value>. See the
"Running Glide From the Command Line" chapter in the
Glide User Manual for a description of available
options.
-affinity Use Glide to calculate the non-covalent binding
affinity
-strain, -calc_strain
Calculate Ligand Strain
-mmgbsa, -calc_mmgbsa
Calculate MMGBSA interaction energy
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:
-NJOBS NJOBS Divide the overall job into NJOBS subjobs.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried
RETRIES times. (Default: 2)
-NOLAUNCH Set up subjob inputs, but don't run the jobs.
Restart Options:
-restart_file RESTART_FILES
Output of a partially completed subjob; keyword may be
used multiple times, once per partial subjob
-RESTART Run 'restart_file' automatically by guessing the names
of the files to use