cphmd_calc_pka.py Command Help

Command: $SCHRODINGER/run -FROM scisol cphmd_calc_pka.py

usage: cphmd_calc_pka.py [-h] -p PREFIX -outprefix OUTPREFIX [-pka0 PKA0]
                         [-n0 N0] [-xcolid XCOLID] [-ycolid YCOLID] [-protS]

Program for calculating pKa by fitting titration curves. Run in the directory
where the constant pH MD simulation was run. This directory must contain
<prefix>_site*.txt files, one per pH.

options:
  -h, --help            show this help message and exit
  -p PREFIX, -prefix PREFIX
                        Prefix for input lambda statistics files
  -outprefix OUTPREFIX  Prefix for output pKa files
  -pka0 PKA0            Initial pKa value (default: pH where the S value is
                        the closest to 0.5)
  -n0 N0                Initial hill coeficient (default: 1.0)
  -xcolid XCOLID        Colid for pH (default: 1)
  -ycolid YCOLID        Colid for deprotonation fraction (default: 3)
  -protS                Input S fraction is for the protonated state