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]
       [-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]
       [-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)
  -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/bozhang/.schrodinger/
                        matsci_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)

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)