protassign Command Help

Command: $SCHRODINGER/utilities/protassign

Protein Assignment Script

Usage: protassign [options] <input-MAE> <output-MAE>

Options:
  -j                Name for the job
  -noflip           Do not sample ASN/GLN/HIS Chi flips
  -nowater          Do not sample water orientations
  -nopropka         Do not use PROPKA for protonation states
  -label_pkas       Label residues with PROPKA pKas
  -asl              ASL expression for which residues to sample (default="all")
  -noprot_asl       ASL expression for which residues to retain input protonation state
  -d                Print debugging information
  -pH               pH at which to sample
  -propka_pH        pH to use with PROPKA ('auto' will attempt to autodect, and use 7.0
                      otherwise)
  -xtal             Use crystal symmetry
  -include_epik_states
                    Include Epik embedded ligand states during optimization
  -f <res> <state>  Force a particular residue to adopt the specified state
                      Mulitple -f specifications are permitted
                      <res> is specified as <chain>:<resnum><ins-code>
                      <state> is one of the following:
                        For HIS:
                          HID         : delta form
                          HIE         : epsilon form
                          HIP         : protonated form
                          "Flip HID"  : flipped delta form
                          "Flip HIE"  : flipped epsilon form
                          "Flip HIP"  : flipped protonated form
                        For ASN/GLN:
                          Flip        : flipped form
                          "No Flip"   : unflipped form
                        For ASP/GLU:
                          Charged     : ionized form
                          "Neutral 1" : protonated on OE1
                          "Neutral 2" : protonated on OE2
                      Example:
                        protassign -f A:116 HIP -f A:124B "No Flip" input.maegz output.maegz
  -minimize         Minimize hydrogens of altered species
  -seed <int>       Seed the random number generator

Job control options:
  -HOST <host>     - Run job on <host> (Default: localhost)
  -LOCAL           - Run in the local directory (obsolete)
  -NOLOCAL         - Run in scratch directory (localhost jobs)
  -WAIT            - Do not return until the job completes
  -NOJOBID         - Run the without jobcontrol (previously -NO_REDIRECT)
  -h or -help      - Print this message and exit