packmol_driver.py Command Help

Command: $SCHRODINGER/run structured_liquid_gui_dir/packmol_driver.py

usage: $SCHRODINGER/run structured_liquid_gui_dir/packmol_driver.py
       [-h]
       [-packmol_input_files PACKMOL_INPUT_FILES [PACKMOL_INPUT_FILES ...]]
       -structure_file STRUCTURE_FILE STRUCTURE_FILE -box_lengths BOX_LENGTHS
       BOX_LENGTHS BOX_LENGTHS [-no_prep_md] [-force_field FORCE_FIELD]
       [-enable_metal_force_field] [-cgffld_loc_type {installed,local}]
       [-water_fftype WATER_TYPE] [-allow_ring_spears]
       [-penalty_factor_ring_spears PENALTY_FACTOR_RING_SPEARS]
       [-radius_factor_ring_spears RADIUS_FACTOR_RING_SPEARS] [-prefer_forced]
       [-HOST <hostname>] [-JOBNAME JOBNAME]

Driver for running packmol. Copyright Schrodinger, LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -packmol_input_files PACKMOL_INPUT_FILES [PACKMOL_INPUT_FILES ...]
                        Specify packmol input *inp files. (default: None)
  -structure_file STRUCTURE_FILE STRUCTURE_FILE
                        Specify a structure file for any *pdb files referenced
                        in other input files. This flag can be used multiple
                        times. Values are two strings, the first is the *mae
                        file containing the structure while the second is the
                        *pdb file name referenced in the other input files.
                        Structures can be atomistic or coarse-grained but all
                        must be one or the other. (default: None)
  -box_lengths BOX_LENGTHS BOX_LENGTHS BOX_LENGTHS
                        Specify in Angstrom the lengths of the a-, b-, and c-
                        lattice vectors that define the periodic boundary
                        condition for the output cells. This flag should be
                        specified for each of the specified input files.
                        (default: None)
  -no_prep_md           By default an input Desmond *cms file is prepared for
                        each packmol output file. Use this option to instead
                        only write the outputs to *mae files. (default: False)
  -force_field FORCE_FIELD
                        Specify the force field to use if preparing Desmond
                        *cms files. For atomistic systems valid force fields
                        are OPLS_2005, S-OPLS and SPFF For coarse-grained
                        systems specify the name of a coarse-grained force
                        field (see related location type flag
                        -cgffld_loc_type.) (default: S-OPLS)
  -enable_metal_force_field
                        Use the metal force field for metal atoms. This is
                        only relevant if using OPLS5, and if not specified
                        then the standard OPLS5 force field will be used for
                        all atoms including metals. (default: False)
  -cgffld_loc_type {installed,local}
                        Location type for a specified coarse-grained force
                        field. Option "installed" means from a standard
                        location in the Schrodinger installation while option
                        "local" means either from /Users/aoza/.schrodinger/mat
                        sci_templates/coarse_grain_force_field_parameters or
                        the job launch directory, i.e. the CWD. (default:
                        local)
  -water_fftype WATER_TYPE
                        Force field type for water molecules. Must be used
                        with -split_components. If using "none", the Residue
                        Name atom property is used instead. (default: SPC)
  -allow_ring_spears    Allow ring-spears in output structures. (default:
                        False)
  -penalty_factor_ring_spears PENALTY_FACTOR_RING_SPEARS
                        If not allowing ring-spears then attempt to prevent
                        them by adding a dummy atom to the center of each ring
                        and for these atoms and the ring atoms scale the
                        weight of the atom-atom distance penalty function by
                        this factor. (default: 10)
  -radius_factor_ring_spears RADIUS_FACTOR_RING_SPEARS
                        If not allowing ring-spears then attempt to prevent
                        them by adding a dummy atom to the center of each ring
                        and for these atoms and the ring atoms scale the
                        radius of the atom-atom distance penalty function by
                        this factor. (default: 1)
  -prefer_forced        If a Packmol output file name marked with "_FORCED"
                        can be found then choose it as the representative
                        Packmol output file from which to read the final
                        structure. Otherwise choose the standard Packmol
                        output file. In the event of packing to high density
                        both files may be present in which case the standard
                        one may relax constraints to remove clashes while the
                        forced one obeys constraints but may have clashes.
                        (default: False)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)