pdb2amber

Generate an AMBER prmtop file from a pdb file.

Introduction

OpenMM offers an excellent concept that the potential energy of the system can be calculated with the pdb file since the standard forcefields are provided internally. In special cases where non-standard amino acids and ligands are in the pdb file, we need to provide additional forcefields. Here, 'build_forcefield' introduces how to build an OpenMM forcefield file (in a xml file) from an AMBER prmtop file. With these additional OpenMM forcefield files, we generate an AMBER prmtop file from a PDB file.

Note

_topology.py, _pdbfile.py, and _forcefield.py were modified codes of topology.py, pdbfile.py, and forcefield.py at the directory of (...)/site-packages/simtk/openmm/app for this goal.

Howto

python pdb2amber.py -i input.json

---`input.json'---

{
    "fname_pdb" : "abc.pdb",
    "fname_prmtop" : "abc.prmtop",
    "fname_ff" : [
        "./data/protein.ff14SB.xml",
        "./data/wat_opc3.xml"
    ]
}