ffbuilder Command Help

Command: $SCHRODINGER/ffbuilder

usage: $SCHRODINGER/ffbuilder [-h] [-project <zip>] [-skip_proj_qm]
                              [-analyze_only] [-verbose] [-RETRIES RETRIES]
                              [-HOST <hostname>[:<n>]] [-OPLSDIR OPLSDIR]
                              [-JOBNAME JOBNAME] [-help_advanced]
                              [input_file]

Force Field Builder driver which runs the following workflow:
- Identify missing torsion parameters, and fragmentize input ligands accordingly
- Run corresponding QM calculations
- Perform fitting to obtain new parameters

On completion, an output OPLS directory is returned as <jobname>_oplsdir/,
containing the new parameters combined with previously developed parameters
provided via -OPLSDIR. Additionally, an archive of the force field builder
project is returned as <jobname>.zip

To merge the new parameters into an existing custom OPLS directory <oplsdir>,
from the command line::

    $SCHRODINGER/utilities/custom_params merge <jobname>_oplsdir/ <oplsdir>/

Copyright Schrodinger LLC, All Rights Reserved.

positional arguments:
  input_file            Input ligands to be analyzed for torsion parameters.

options:
  -h, --help            show this help message and exit
  -project <zip>        Input archive with existing ffbuilder project data.
                        Backwards compatible with directory format.
  -skip_proj_qm         In the case of an incompatible project, missing or
                        failed QM calculations in the project input may be
                        retried. Pass skip_proj_qm to skip retrying these QM
                        calculations. Requires the -project arg.
  -analyze_only         Force field builder returns after the analysis stage.
                        This provides a preview of fragments and skips
                        potentially time-consuming QM calculations and
                        parameter fitting.
  -verbose              Enable verbose logging.
  -help_advanced        Show advanced options help message and exit.

Standard Options:
  -RETRIES RETRIES      If a subjob fails for any reason, it will be retried
                        RETRIES times.

Job Control Options:
  -HOST <hostname>[:<n>]
                        Run job remotely on the indicated host entry with up
                        to <n> simultaneous subjobs. If <n> is not specified,
                        the default number of processors from the host entry
                        is used if submitting to a queueing system, or a
                        single processor for a host entry without a queue
                        (localhost).
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
  -JOBNAME JOBNAME      Provide an explicit name for the job.