trajectory_analyze_hbonds.py Command Help

Command: $SCHRODINGER/run trajectory_analyze_hbonds.py

usage: trajectory_analyze_hbonds.py [-h] [-asl2 ASL2] [-dist DIST]
                                    [-min_da MIN_DA] [-min_aa MIN_AA]
                                    [-max_aa MAX_AA]
                                    infile outfile asl

Records the number of hydrogen bonds in each frame of a trajectory within the
user-provided ASL expression.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  infile          Desmond trajectory file. The file must end with -out.cms.
  outfile         Output analysis file. Output is written in csv format.
  asl             ASL expression defining the whole/first set of atoms whose hydrogen bonds you want to analyze. The expression should be enclosed in quotes. E.g. '(res.num 722)' or '(res.num 722) OR (res.num 802)'

options:
  -h, --help      show this help message and exit
  -asl2 ASL2      ASL expression defining the second set of atoms whose hydrogen bonds you want to analyze. The expression should be enclosed in quotes. E.g. '(res.num 802)'. This is optional.
  -dist DIST      Maximum allowable bond distance. Default=2.8
  -min_da MIN_DA  Minimum allowable donor angle. Default=120.0
  -min_aa MIN_AA  Minimum allowable acceptor angle. Default=90.0
  -max_aa MAX_AA  Maximum allowable acceptor angle. Default=360.0