Gentop

The pmx gentop script can be used to fill out the B states for a topology file containing hybrid residues. You can obtain such topology by running the Gromacs command pdb2gmx on a structure file generated with the pmx mutate command.

$ pmx gentop -h
usage: pmx [-h] [-p topol] [-o outfile] [-ff ff] [--split] [--scale_mass]
           [--norecursive]

This script fills in the B state to a topology file (itp or top) according to
the hybrid residues present in the file. If you provide a top file with
include statemets, by default the script will run through the included itp
files too; this can turned off using the --norecursive flag. You need to use
this script after having mutated a structure file with pmx mutate, and after
having passed that mutated structure through pdb2gmx.

optional arguments:
  -h, --help     show this help message and exit
  -p topol       Input topology file (itp or top). Default is "topol.top"
  -o outfile     Output topology file. Default is "pmxtop.top"
  -ff ff         Force field to use. If -p is a top file, it is not necessary
                 to specify the forcefield, as it will be determined
                 automatically. If -p is an itp file, then -ff is needed, and
                 if it not provided a list of available ff will be shown.
  --split        Write separate topologies for the vdW and charge
                 transformations.
  --scale_mass   Scale the masses of morphing atoms so that dummies have a
                 mass of 1.
  --norecursive  Whether to fill the B states also for all itp files included
                 in the provided topology file. Default is True. This flag
                 sets it to False.