coarse_grain_backmapping_driver.py Command Help

Command: $SCHRODINGER/run coarse_grain_backmapping_gui_dir/coarse_grain_backmapping_driver.py

usage: $SCHRODINGER/run coarse_grain_backmapping_gui_dir/coarse_grain_backmapping_driver.py
       [-h] [-forcefield FORCE_FIELD] [-md_temp MD_TEMP] [-md_time MD_TIME]
       [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT] [-seed SEED]
       [-md_umbrella] [-force_c FORCE_C] [-water_fftype WATER_TYPE]
       [-HOST <hostname>] [-D] [-JOBNAME JOBNAME]
       input_file

Backmapping driver to convert CG structures to AA and run constrained MD
relaxation of the backmapped structure. The script takes a CG structure as
input, and the output is a relaxed AA structure in CMS. We further perform
stereo refinement for stereo centers in the backmapped structure by applying
restraints to the original stereo centers and running a short constrained MD
simulation. Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input coarse-grained structure file.

options:
  -h, -help             Show this help message and exit.
  -forcefield FORCE_FIELD
                        The backmapped structure will be created with the
                        specified forcefield. If not specified, the default
                        forcefield is OPLS_2005. OPLS5 forcefield is not
                        supported for backmapping. (default: OPLS_2005)

Simulation options:
  -md_temp MD_TEMP      Temperature (in K) of the simulations. (default:
                        300.0)
  -md_time MD_TIME      MD time (in ns) of the simulation. (default: 10.0)
  -md_timestep MD_TIMESTEP
                        MD time step (in fs) of the simulations. (default:
                        1.0)
  -md_trj_int MD_TRJ_INT
                        MD trajectory recording interval (in ps). (default:
                        10.0)
  -seed SEED            Seed for random number generator. (default: 1234)
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -force_c FORCE_C      Force constant (kcal mol-1 Å-2) to use for the
                        substrate positional restraints. (default: 1.0)
  -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)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)