fep_plus Command Help
Command: $SCHRODINGER/fep_plus
usage:
* Run a new job:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> <pv-or-fmp-file>
* Restart a previously interrupted job:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> -RESTART -checkpoint <multisim-checkpoint-file>
* Extend production simulations for certain edges:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> -extend <edge-file> -checkpoint <multisim-checkpoint-file>
An example for the format of an edge-file:
36da5ad:397128e
33dd5ad:347118e
33fe5ad:3171f8e
Each line specifies an edge with the two node's IDs. Each node ID is a hex
number of at least 7 digits. The two IDs are separated by a ':' (or '-' or
'_').
* Prepare input files for multisim. Do NOT run job:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> <pv-or-fmp-file> -prepare
* Run a protein residue mutation job (stability-inclusive):
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> <mae-file> -protein <mutation-file> -solvent_asl <SOLVENT-ASL>
<mutation-file> follows the same format as used by $SCHRODINGER/run residue_scanning_backend.py -muts_file
* Run a protein stability-only job:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> <mae-file> -protein <mutation-file>
* Add mutations to a complete protein fep job:
$SCHRODINGER/fep_plus <out-fmp-file> -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> -protein <mutation-file> -expand_protein <mae-file>
* Run protein FEP with pre-built mutant structures:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> <mae-file> -protein <mutation-file> -mutant-structures-file <mutant-structures-file>
* Run a metalloprotein FEP job:
$SCHRODINGER/fep_plus -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> <pv-or-fmp-file> -mp <property-name>
positional arguments:
inp_file A fmp or a pv structure file
options:
-h, --help show this help message and exit
-ff {OPLS4|OPLS5} Specify the forcefield to use. Default: OPLS4.
-seed <integer> Specify seed of pseudorandom number generator for
initial atom velocities. Default: 2014.
-ppj PPJ Specify number of processors per job, which strictly
corresponds to the number of CPUs to request. On all
standard cluster configurations, this will also
correspond to the number of GPUs requested per job, as
Desmond will use one GPU per CPU. Default: 1.
-checkpoint <multisim-checkpoint-file>
Specify the multisim checkpoint file.
-prepare Do not run job. Only prepare multisim input files.
-JOBNAME <string> Specify the job name.
-buffer <real> Specify a larger buffer size (in Angstroms). Defaults:
5 in complex leg, 5 in solvent leg of protein-residue-
mutation FEP, 10 in solubility FEP, 10 in solvent leg
of other types of FEP, 10 for protein-protein
interactioncalculations, 8.0 for kinetics calculations
and 10.0 for kinetics calculations with membrane. The
custom value will be used only if it's greater than
the corresponding default values.
-maxjob <integer> Maximum number of simultaneous subjobs. Default: 0
(unlimited)
-lambda-windows <integer>, -lambda_windows <integer>
Number of lambda windows for the default protocol.
Default: 12.
-ffbuilder Run the ffbuilder workflow.
-ff-host <string> Host for the ffbuilder jobs specified as
HOST:MAX_FF_BUILDER_JOBs. This must be set if using
-ffbuilder.
-energy-groups Compute energy groups during production simulations.
-enable-metal-force-field
Enable metal support for the OPLS5 force field.
-salt <real> Add salt to simulation box with default or specified
salt concentration (in M). Charged protocol will
always have a minimum of 0.15 M salt added. Default:
0.0 (only adds 0.15 M salt to charged protocol).
-no-batch-replica-subjobs
If set, disables batch replica subjobs. Each lambda
window will be launched as its own job.
-ensemble {muVT|NPT|NVT}
Specify the ensemble class. Default: muVT.
-time <sim-time> Specify the production-simulation time (in ps). For
extension, this option specifies the additional
simulation time (in ps). For new jobs - Default:
5000.0 Min value: 500.0. For extension - Default:
5000.0 Min value: 0.0.
-equilibration-time <equilibration-time>
Specify simulation time for the unrestrained
equilibration of the complex leg prior to FEP (in ps).
For the muVT ensemble, the default complex leg
equilibration time is 20.0 ps. Otherwise, the default
equilibration time is 240.0 ps.
-time-complex <sim-time>
Specify the production-simulation time (in ps) for the
complex leg of the FEP stage. If provided, this value
will override -time for this leg. For extension, this
option specifies the additional simulation time (in
ps). For new jobs - Default: 5000.0 Min value: 500.0.
For extension - Default: 5000.0 Min value: 0.0.
-time-solvent <sim-time>
Specify the production-simulation time (in ps) for the
solvent leg of the FEP stage. If provided, this value
will override -time for this leg. For extension, this
option specifies the additional simulation time (in
ps). For new jobs - Default: 5000.0 Min value: 500.0.
For extension - Default: 5000.0 Min value: 0.0.
-time-vacuum <sim-time>
Specify the production-simulation time (in ps) for the
vacuum leg of the FEP stage. If provided, this value
will override -time for this leg. For extension, this
option specifies the additional simulation time (in
ps). For new jobs - Default: 5000.0 Min value: 500.0.
For extension - Default: 5000.0 Min value: 0.0.
-time-fragment <sim-time>
Specify the production-simulation time (in ps) for the
fragment leg of the FEP stage. If provided, this value
will override -time for this leg. For extension, this
option specifies the additional simulation time (in
ps). For new jobs - Default: 5000.0 Min value: 500.0.
For extension - Default: 5000.0 Min value: 0.0.
-protein <mutation> Generate and run protein residue mutation if a
mutation_file is given here and a solvent_asl is also
provided; Generate and run protein stability when a
mutation_file is given here and no solvent_asl is
provided
-mp <property_name> Generate and run metalloprotein workflow by specifying
the atom property used to indicate the atoms involved
in the zero order bond. Pass in option multiple times
to specify multiple mp properties.
-mutation-chain-asl <asl-string>
Specify ASL of the substructure where mutations occur
for selectivity jobs in protein residue mutation FEP
workflow.
-vacuum Include vacuum simulations. Only supported for small
molecule FEP.
-extend <edge-file> Extend production simulations of specified edges.
-atom-mapping <string>, -atom_mapping <string>
Atom mapping specification for leadoptmap.py. For
small molecule FEP, specify SMARTS string to customize
core assignment; for protein residue mutation FEP,
'sidechain' is the only argument allowing the side
chain atoms to be mapped as well while by default the
side chains are not mapped. This option will be
ignored if fmp file is provided as input.
-modify-dihe, -modify_dihe
Scale the torsion energies in the perturbation region
to improve sampling.
-no-h-mass, -no_h_mass
Turn off hydrogen mass repartitioning (on by default).
-membrane Indicates the model system is a membrane protein
system, such as the GPCR. If membrane/water components
are not provided, the POPC bilayer will be added and
equilibrated. The protein coordinates should be OPM-
compatible. If membrane/water components are provided,
this option is enabled automatically.
-charged-lambda-windows <integer>, -charged_lambda_windows <integer>
Number of lambda windows for the charge protocol.
Default: 24
-core-hopping-lambda-windows <integer>, -core_hopping_lambda_windows <integer>
Number of lambda windows for the core-hopping
protocol. Default: 16
-residue-structure <mae-file>, -residue_structure <mae-file>
Noncanonical amino acids for protein mutation.
-expand-protein EXPAND_PROTEIN, -expand_protein EXPAND_PROTEIN
Pass the structure file for protein fep to re-run with
additional mutations.
-mutant-structures-file <mae-file>, -mutant_structures_file <mae-file>
Structure file containing pre-built mutant structures.
When provided, Prime mutation generation will be
skipped.
-water <string> Specify the water model used in the simulations. Valid
values: SPC, SPCE, TIP3P, TIP3P_CHARMM, TIP4P,
TIP4PEW, TIP4P2005, TIP5P, TIP4PD. Default: SPC
-custom-charge-mode <string>, -custom_charge_mode <string>
Set the custom charge calculation mode. Default is to
'assign' custom charges based on the input geometries
to detected ligands. Set to 'clear' to clear custom
charges without assigning them. Set to 'keep' to keep
existing custom charge parameters. The following FEP
types support 'assign' in subjobs containing ligand
structures: ligand_selectivity, prm_ligand_binding,
small_molecule
-skip-leg <leg_name> Specify the legs to skip
(complex/solvent/vacuum/fragment). Pass in multiple
times to skip multiple legs
-restraints-file <restraints-file>
Apply positional restraints to the receptor as
specified in the file provided. NOTE: Depending on the
workflow, the term 'receptor' can refer to a protein,
nucleic acids, or a ligand. The file should give the
restraints in Ark format, e.g., a file could contain:
restraints={existing=ignore new=[{atoms='asl:(protein
and backbone and not a.ele H)' force_constants=[1.0
2.0 3.0] name=posre_harm}]}
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-LOCAL Do not use a temporary directory for job files. Keep
files in the current directory.
-D, -DEBUG Show details of Job Control operation.
-TMPDIR TMPDIR The name of the directory used to store files
temporarily during a job.
-SAVE Return zip archive of job directory at job completion.
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
Standard Options:
-SUBHOST <hostname> or -SUBHOST <hostname:nproc> or -SUBHOST "hostname1:nproc1 ... hostnameN:nprocN"
Run the subjobs on the specified hosts. The driver is
run on the host specified with -HOST.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried
RETRIES times.
-RESTART Restart a previously failed job, utilizing any already
completed subjobs.