ifd-md Command Help
Command: $SCHRODINGER/ifd-md
usage: $SCHRODINGER/ifd-md [-h] -template_complex TEMPLATE_COMPLEX
[-template_wmap TEMPLATE_WMAP] -target_ligand
TARGET_LIGAND -ligand_asl LIGAND_ASL
[-jobname JOBNAME] -cpu_subhost CPU_SUBHOST -n_cpu
N_CPU -gpu_subhost GPU_SUBHOST -n_gpu N_GPU
[-no_md] [-no_mtd] [-em_map_fn EM_MAP_FN]
[-keep_best_poses FILTERFUNC | -filter_by_score FILTERFUNC | -filter_by_zscore FILTERFUNC]
[-run_ffbuilder] [-overwrite] [-no_cleanup]
[-res_include_file RES_INCLUDE_FILE] [-rxn RXN]
[-rxn_receptor_res RXN_RECEPTOR_RES]
[-rxn_ligand_asl RXN_LIGAND_ASL]
[-custom_rxn_file CUSTOM_RXN_FILE]
[-rxn_chirality {R,S}] [-membrane [ref_structure]]
[-add_membrane_equilibration_time ADD_MEMBRANE_EQUILIBRATION_TIME]
[-OPLSDIR OPLSDIR] [-RETRIES RETRIES] [-v]
[-HOST <hostname>] [-WAIT] [-D] [-NOJOBID]
[-NOLAUNCH]
options:
-h, --help show this help message and exit
-template_complex TEMPLATE_COMPLEX
A template ligand/receptor complex. The template
ligand will be used to identify the binding site and
for pharmacophore overlap with the target ligand. The
template receptor will undergo induced fit changes.
-template_wmap TEMPLATE_WMAP
A watermap run on the template complex. It should be
run with a sufficently large ligand distance, 10 A for
example, to accommodate the target ligand and any
conformational diversity. If not provided, one will be
generated.
-target_ligand TARGET_LIGAND
Target ligand to be induced fit docked into the
template complex.
-ligand_asl LIGAND_ASL
ASL to identify the template ligand in the
template_complex.
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Set the base name of outputs
-cpu_subhost CPU_SUBHOST
Subhost for CPU jobs
-n_cpu N_CPU Number of CPUs to use.
-gpu_subhost GPU_SUBHOST
Subhost for GPU jobs
-n_gpu N_GPU Number of GPU to use
-no_md Skip any MD jobs. This flag will ignore the values for
-gpu_subhost and -n_gpu.
-no_mtd Will stop the workflow before the MtD stage. Running
only the 500 ps MD.
-em_map_fn EM_MAP_FN, -EM_MAP_FN EM_MAP_FN
If this option is included, phasedock poses will be
filtered by density score based on this EM map, and
GlideEM will be run in place of Glide stages.
-keep_best_poses FILTERFUNC
-filter_by_score FILTERFUNC
-filter_by_zscore FILTERFUNC
-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.
-overwrite Overwrite any existing job outputs. This will cause
all jobs to rerun
-no_cleanup Do not perform any cleanup actions
-res_include_file RES_INCLUDE_FILE
A file containing residues to add to refinement list.
Residues are of the form chain:resnum or
chain:resnum:inscode. One residue should be specified
per line.
-v show program's version number and exit
Covalent Docking Options:
-rxn RXN Name for one of the standard reaction types. The list
of all available standard reaction types can be
accessed by running: $SCHRODINGER/covalent_docking
-print_named_reactions. The reaction name must be
enclosed within quotation marks (e.g., "Michael
Addition")
-rxn_receptor_res RXN_RECEPTOR_RES
PSP style residue label for the reactive residue in
the receptor (e.g. 'A:345')
-rxn_ligand_asl RXN_LIGAND_ASL
ASL defining the reactive ligand atom if there is more
than one possible reactive site
-custom_rxn_file CUSTOM_RXN_FILE
Custom reaction file. -rxn does not need to be set if
this option is used (will automatically be set to
'Custom')
-rxn_chirality {R,S} If applicable, specification for the stereochemistry
introduced by the covalent bond formation
Membrane Protein Options:
-membrane [ref_structure]
Enable explicit membrane MD. Argument can be a
reference structure to orient IFD-MD structures before
building the membrane, and must have a ct-level
property defining the membrane thickness in Angstrom
named 'r_pdb_OPM_membrane_thickness'. PDBs obtained
from OPM will automatically create this property when
parsed. Alternatively, if no file is passed as an
argument, it is assumed that the template complex is
pre-oriented relative to the membrane. In this case,
the template complex can also provide a thickness
property value, or it will be set to a default value
of 34.25.
-add_membrane_equilibration_time ADD_MEMBRANE_EQUILIBRATION_TIME
Additional membrane equilibration (in ps) to perform
prior to the 500 ps MD (default: 0)
Job Control Options:
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
Standard Options:
-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.