fep_residue_scanning Command Help

Command: $SCHRODINGER/fep_residue_scanning

usage: 
Run protein residue scanning using lambda dynamics backend.

* Run a new job:
    $SCHRODINGER/fep_residue_scanning input.mae -mutations-file <mutations-file> -HOST <job-host> -JOBNAME <jobname>

* Run a job with non-standard amino acids after generating pmf coefficients:
    $SCHRODINGER/fep_residue_scanning input.mae -mutations-file <mutations-file> -pmf-coefficients <pmf-coefficients-file> -residue-structure <residue-structure-file> -HOST <job-host> -JOBNAME <jobname>

* Restart a previously interrupted job:
    $SCHRODINGER/fep_residue_scanning input .mae -HOST <job-host> JOBNAME <jobname> -RESTART

positional arguments:
  inp_file              A Maestro structure file

options:
  -h, --help            show this help message and exit
  -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.
  -prepare              Do not run job. Only prepare multisim input files.
  -JOBNAME <string>     Specify the job name.
  -maxjob <integer>     Maximum number of simultaneous subjobs. Default: 0
                        (unlimited)
  -energy-groups        Compute energy groups during production simulations.
  -time <sim-time>      The time (in ps) for the production simulation stage,
                        not including adaptive sampling. The total production
                        simulation time is given by <time> + <adaptive
                        sampling time>. Default: 5000.0.
  -adapt-interval <real>
                        The interval (in ps) for the adaptive sampling in the
                        replica exchange stage. Default: 2000.0.
  -adapt-iterations <integer>
                        The number of iterations for the adaptive sampling in
                        the replica exchange stage; the total adaptive
                        sampling time is given by
                        adapt_interval*adapt_iterations. Default: 4.
  -adapt-linear         Update the first order coefficients for the adaptive
                        sampling in the replica exchange stage. Default:
                        False.
  -reset-configuration  Reset the configuration (microstate) to its initial
                        state at every adaptive iteration for the adaptive
                        sampling in the replica exchange stage. If not
                        specified, trajectory continues as normal. Default:
                        False.
  -mutations-file <mutation>
                        A file containing a list of mutations.
  -pmf-coefficients <pmf coefficients>
                        A file containing a database of pmf coefficients.
  -replica-interval <real>
                        The sampling interval of the relative population (to
                        run simulations at) between the wild type and the
                        mutant in the logarithm 10 base scale. e.g. a value of
                        1.0 indicates a 10-fold change in relative population.
                        Default: 1.0
  -total-replicas <integer>
                        The total number of replicas to simulate. Default: 12
  -mutation-chain-asl <mutation-chain-asl>
                        The ASL to select the protein chain to mutate.
  -ensemble {muVT|NPT}  Specify the ensemble class for simulation. Defualt:
                        muVT.
  -residue-structure <mae-file>
                        Non-standard amino acids for protein mutation. If
                        specified, a the -pmf-coefficients option must also be
                        supplied.
  -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: lambd_prm_ligand_binding

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.