dps angle

Calculate backbone-angle profiles and time series for equivalent protein chains.

Synopsis and options

usage: dps angle [-h] -s FILE -f FILE [-n FILE] [-sel SELECTION] [-b START_TIME] [-e END_TIME]
                 [-dt DELTA_TIME] [-pbc] [-ot FILE] [-or FILE] [-ors FILE] [-ov FILE]

Calculate backbone-angle profiles and time series for equivalent protein chains.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing the system and simulation
                        settings. (required)
  -f FILE, --input FILE
                        Input trajectory file (.xtc). (required)
  -n FILE, --index FILE
                        Optional index file (.ndx) defining additional atom groups. (default:
                        None)

Output:
  -ot FILE, --output-time FILE
                        Output chain-averaged angle time series (.xvg); the extension is added if
                        omitted. (default: None)
  -or FILE, --output-residue FILE
                        Output time-averaged angle profile by residue (.xvg); the extension is
                        added if omitted. (default: None)
  -ors FILE, --output-residue-statistic FILE
                        Output residue-wise angle mean and standard deviation (.xvg); the
                        extension is added if omitted. (default: None)
  -ov FILE, --output-verbose FILE
                        Output per-chain, per-residue angle time series (.xvg); the extension is
                        added if omitted. (default: None)

Parameters:
  -h, --help            Show this help message and exit.
  -sel SELECTION, --selection SELECTION
                        Index group containing angle-center beads; chains are split and terminal
                        beads are ignored. If omitted, prompt interactively. (default: None)
  -b START_TIME, --start-time START_TIME
                        First trajectory time to analyze, in ns. (default: None)
  -e END_TIME, --end-time END_TIME
                        Last trajectory time to analyze, in ns. (default: None)
  -dt DELTA_TIME, --delta-time DELTA_TIME
                        Approximate interval between analyzed frames, in ns. (default: None)
  -pbc, --treat-pbc     Unwrap molecules across periodic boundaries before analysis. (default:
                        False)

Examples:
  dps angle -s run.tpr -f run.xtc -or angles-by-residue.xvg

Note

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