Genlib

The pmx genlib script helps in the generation of the pmx alchemical force field libraries. It automates the steps needed to create and/or extend the rtp, mtp, atp, and itp files used by Gromacs. Because every force field has its own peculiarities, which the script might not always take into account, this command is not recommended to the average user. Expert users who use it should remember to always check manually that the files generated are correct, and ideally to verify the correctness of the library via single point energy calculations of the end states for all hybrid residues.

$ pmx genlib -h
usage: pmx [-h] [-f1 ipdb1] [-f2 ipdb2] [-o1 opdb1] [-o2 opdb2]
       [--ffpath ffpath] [--fatp fatp] [--fnb fnb] [--moltype moltype]
       [--noalign] [--cbeta] [--noH2H] [--log log]

The script creates hybrid structure and topology database entries (mtp and rtp)
in order to generate a pmx alchemical force field library.

The easiest way to generate the library is to call this script from within
the folder of the force field you are interested in.

If two pdb files (aligned on the backbone) are provided, the hybrid pdb, mtp,
and rtp files are written to file. If no pdb input file is provided,
the script uses pregenerated residues in order to build hybrid pdb, mtp, and
rtp files for all possible residue pairs, thus preparing the whole pmx ff
library.

In addition, atomtype (-fatp) and non-bonded parameter (-fnm) files for the
introduced dummy atoms are generated. By default, these point towards the
files already present in the forcefield. In this way, the additional parameters
for the dummies are appended to the existing ff file, rather than being
written to new files.

optional arguments:
    -h, --help         show this help message and exit
    -f1 ipdb1          First input PDB file. Default is none provided.
    -f2 ipdb2          Second input PDB file. Default is none provided.
    -o1 opdb1          First output PDB file. Default is none provided.
    -o2 opdb2          Second output PDB file. Default is none provided.
    --ffpath ffpath    Path to mutation forcefield. Default is current folder.
    --fatp fatp        Atom types (atp) file. If the file is
                       present, data is appended to it, otherwise a new
                       file is created. Default is "atomtypes.atp".
    --fnb fnb          Non-bonded (nb) types file. If the file is
                       present, data is appended to it, otherwise a new
                       file is created. Default is "ffnonbonded.itp".
    --moltype moltype  The type of molecule for which the library is
                       being built. Available options are "protein", "dna",
                       or "rna". Default is "protein".
    --noalign          Whether to align the sidechains of the two
                       input PDB files provided. Default it True; this flag
                       sets it to False.
    --cbeta            Whether to morph sidechain between the two
                       residues or to use dummy atoms to (de)couple the
                       whole sidechain. By default, sidechain atoms are
                       morphed so to minimise the size of the perturbation.
                       With this flag set, whole sidechains are (de)coupled
                       instead; i.e. all atoms after C-beta are not mapped
                       between the two residues.
    --noH2H            Whether to allow hydrogen to/from heavy atoms
                       morphing. Default is True, this flag sets it to False.
    --log log          Logging level. Either "info" or "debug". Default is "info".