mmml pycharmm-two-residue-sample¶
Restrained sampling for two-residue CHARMM system.
Usage¶
mmml pycharmm-two-residue-sample --help
Options¶
usage: mmml pycharmm-two-residue-sample [-h] --pdbfile PDBFILE [--cell CELL]
[--skip-setup-energy-show]
[--pycharmm-minimize-steps N]
[--output-pdb OUTPUT_PDB]
[--two-residue-restraint-force K]
[--two-residue-restraint-r0 ANGSTROM]
[--two-residue-sampling-steps N]
[--two-residue-restraint-resid1 TWO_RESIDUE_RESTRAINT_RESID1]
[--two-residue-restraint-resid2 TWO_RESIDUE_RESTRAINT_RESID2]
Set up a two-residue CHARMM system and run restrained sampling.
Input & configuration:
--pdbfile PDBFILE Path to a PDB file containing the two-residue CHARMM
system.
--output-pdb OUTPUT_PDB
Path for sampled coordinates as PDB (default: pdb/two-
residue-sampled.pdb).
--two-residue-restraint-force K
CHARMM harmonic restraint force constant for two-residue
sampling (default: 1.0).
--two-residue-restraint-r0 ANGSTROM
CHARMM harmonic restraint target distance r0 for two-
residue sampling (default: 2.5 Angstrom).
--two-residue-sampling-steps N
ABNR steps for restrained two-residue sampling (default:
--pycharmm-minimize-steps).
--two-residue-restraint-resid1 TWO_RESIDUE_RESTRAINT_RESID1
First CHARMM residue id for two-residue sampling
(default: 1).
--two-residue-restraint-resid2 TWO_RESIDUE_RESTRAINT_RESID2
Second CHARMM residue id for two-residue sampling
(default: 2).
Execution:
--skip-setup-energy-show
Skip energy.show() in setup_box for faster startup.
--pycharmm-minimize-steps N
Fallback ABNR steps when --two-residue-sampling-steps is
not set (default: 1000).
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--cell CELL Cubic cell side length in Angstrom for periodic boundary
conditions (default: 1000).