gopt_to_pdb.py

Help message 

usage: gopt_to_pdb.py [-h] [-gout OUTPUT] [-pdb PDBF] [-frame FRAME] [-name NAME]

generate pdbfiles from 1.out

options:
  -h, --help    show this help message and exit
  -gout OUTPUT  gaussian output file
  -pdb PDBF     template pdb file
  -frame FRAME  select frame: -1 (final=default) or integer or "all"
  -name NAME    filename for output pdb

Inputs

  • -gout: Gaussian output file to extract geometry from (required)
    • Given as filename, default is 1.out
    • Example: -gout file.out
  • -pdb: Template pdb to put optimised geometry into (required)
    • Given as filename
    • Example: -pdb model_N_template.pdb
  • -frame: Which structure from the output to convert
    • Given as integer or ‘all’ or -1 for just the final structure (default)
    • Examples: -frame all or -frame 10
  • -name: base name to use for converted structure

    • Given as string (with or without “.pdb” ending), default is ‘gout’

    • Examples: -name model_13_ts_opt or -name model_13_reactant_opt.pdb

Outputs

  • [name].pdb if making only final frame, [name].f[num].pdb if using -frame all or -frame [num]