jaguar_pka Command Help

Command: $SCHRODINGER/utilities/jaguar_pka

usage:
$SCHRODINGER/utilities/jaguar_pka [options]

options:
  -h            : print help and exit
  -d            : return deprotonated form in Maestro output file
  -j <filename> : specify a .jres file (required)
  -i            : run in identification mode
  -f <name>     : specify functional group parameters to use (to 
                  skip corrections use 'none')
  -m <filename> : specify an alternate pka_match.xml file (default
                  $MMSHARE_EXEC/../../data/jaguar/pka_match.xml)
  -n            : do not allow use of zwitterion functional groups
  -o <filename> : specify a Maestro output file
  -s <solvent>  : specify a solvent