probe_grid_backend.py Command Help

Command: $SCHRODINGER/run probe_grid_gui_dir/probe_grid_backend.py

usage: $SCHRODINGER/run probe_grid_gui_dir/probe_grid_backend.py
       [-h]
       [-keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
       [-probe PROBE] [-probe_charge CHARGE] [-probe_radius ANGSTROMS]
       [-charge CHARGE] [-mult MULTIPLICITY] [-intra INTRA-SURFACE_SPACING]
       [-surfaces NUMBER] [-inter INTER-SURFACE_SPACING]
       [-opt OPTIMIZATION_SET [OPTIMIZATION_SET ...]] [-compile STRUCTURES]
       [-TPP THREADS] [-JOBNAME JOBNAME] [-HOST <hostname>]
       TARGET_STRUCTURE PATH

This is the driver script to run a grid scan of a probe over a target
molecule. Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  TARGET_STRUCTURE      The path to the file holding the target structure to
                        probe.
  PATH                  The path to the output file. This file will contain
                        structures with the computed properties.

options:
  -h, -help             Show this help message and exit.
  -keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...], -k KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
                        Jaguar keywords to include in calculations. Can be
                        given multiple keywords, ex. -k dftname=b3lyp
                        basis=midix... If this is the last flag before the
                        input/output file names, use -- to terminate the list
                        of keywords. (default: )
  -probe PROBE          Identity of the probe. Can be the string "point" to
                        indicate a point charge (default). Alternatively, a
                        single atom probe can be specified using an atomic
                        symbol. Finally, the probe structure can be stored in
                        a file and the path to the file given with this flag.
                        (default: point)
  -probe_charge CHARGE  Charge on the probe. Required if the probe is a point
                        charge, or if CDFT calculations are run. Unused
                        otherwise. For CDFT calculations, the probe is
                        constrained to have a charge of this value, while the
                        target is constrained to have a charge of x - y, where
                        x is given by -charge and y is give by -probe_charge.
                        (default: 0)
  -probe_radius ANGSTROMS
                        The first grid surface will be placed at the VdW
                        surface of the target molecule plus some probe radius.
                        By default, the probe radius is taken as the VdW
                        radius of the probe atom. The VdW radius of a point
                        charge is 0. Use this flag to set the probe radius to
                        some other floating point value. (default: None)
  -charge CHARGE        Charge on the entire system. For point charge probes,
                        do not include the charge of the probe. For all other
                        probes, include the charge of the probe in the total
                        charge. Default is 0. (default: 0)
  -mult MULTIPLICITY    Multiplicity of the entire system. Point charges do
                        not count towards multiplicity. Default is 1.
                        (default: 1)
  -intra INTRA-SURFACE_SPACING
                        Distance, in Angstroms, between grid points on the
                        same surface. Default is 1.0. (default: 1.0)
  -surfaces NUMBER      Number of grid surfaces. Default is 1. (default: 1)
  -inter INTER-SURFACE_SPACING
                        If using more than one surface, each surface will be
                        spaced outward by this amount from the previous
                        surface. Default is 1.0 Angstroms. (default: 1.0)
  -opt OPTIMIZATION_SET [OPTIMIZATION_SET ...]
                        Specify what part of the geometry to optimize. The
                        default of "none" is not to optimize the geometry.
                        "all" will optimize the entire probe-target complex,
                        including the location of the probe. The remaining
                        options will optimize only the specified atoms, and
                        more than one option can be given. "target" optimizes
                        the target geometry. "probe" optimizes the probe
                        geometry. "probe_distance" optimizes the probe-target
                        distance but preserves the probe-target vector.
                        "probe_location" fully optimizes the location of the
                        probe relative to the target, including distance and
                        vector. Note that if this is the last flag, it should
                        be terminated with a "--". Ex. -opt target
                        probe_distance -- (default: none)
  -compile STRUCTURES   The set of structures to compile in the output file.
                        Options are "all", "initial_atom", or "final_atom".
                        "all" will save all results to the output file.
                        "initial_atom" will save only the lowest energy
                        structure for each set of points that start closest to
                        a given atom. "final_atom" will save only the lowest
                        energy structure for each set of points where the
                        probe ends closest to a given atom after geometry
                        optimization. "initial_atom" and "final_atom" are
                        identical unless a geometry optimization is performed.
                        These last two options are useful if only the lowest
                        energy structure probing a given target atom is of
                        interest. (default: all)
  -TPP THREADS          The number of threads to use per Jaguar job (default:
                        1)
  -JOBNAME JOBNAME      Set jobname for this calculation. (default: None)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)