dps genelastic

Add a distance-based elastic network to an ITP topology.

Synopsis and options

usage: dps genelastic [-h] -f FILE -p FILE -o FILE -er FILE [-ef ELASTIC_FORCE_CONSTANT]
                      [-el ELASTIC_LOWER] [-eu ELASTIC_UPPER]

Add a distance-based elastic network to an ITP topology.

Input:
  -f FILE, --structure FILE
                        Input reference structure file (.pdb). (required)
  -p FILE, --topology FILE
                        Input topology file (.itp). (required)
  -er FILE, --elastic-residues FILE
                        Input text file listing one elastic-network bead group per line, using
                        1-based bead indices. (required)

Output:
  -o FILE, --output FILE
                        Output topology file (.itp); the extension is added if omitted. (required)

Parameters:
  -h, --help            Show this help message and exit.
  -ef ELASTIC_FORCE_CONSTANT, --elastic-force-constant ELASTIC_FORCE_CONSTANT
                        Elastic-bond force constant, in kJ mol^-1 nm^-2. (default: 5000)
  -el ELASTIC_LOWER, --elastic-lower ELASTIC_LOWER
                        Lower distance cutoff for elastic bonds, in nm. (default: 0.5)
  -eu ELASTIC_UPPER, --elastic-upper ELASTIC_UPPER
                        Upper distance cutoff for elastic bonds, in nm. (default: 0.9)

Examples:
  dps genelastic -f chain.pdb -p chain.itp -o elastic.itp -er elastic-groups.dat

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps genelastic -h in the installed environment for the same reference at the command line.