CP2K_qmmm_input_preparation_scripts

A compilation of useful python scripts to create QM/MM CP2K inputfiles.

Author: Salomé Llabrés Prat, PhD

This repository contains the following scripts:

cp2krestart2gromacs.py

This script converts CP2K restart file to GROMACS files. It does so following these steps:

1 - Reads CP2K restart file. 2 - Generates a AMBER restart file. 3 - Convert AMBER (.prmtop and .inpcrd) to GROMACS format (.top and .gro) via parmed. 4 - Rewrites GROMACS coordinates to include velocities.

It requires the CP2K restart file and a basename to name the gromacs files. It needs parmed!

It outputs these files:

AMBER restart file: basename.inpcrd GROMACS topology: basename.top GROMACS coordinates: basename.gro GROMACS coordinates + velocities: basename.vel.gro

Usage:

cp2krestart2gromacs [options] infile outfile

cp2kinput2ndxformat.py

This script collects atom indexes outlined in the QM region and link atoms of a CP2K input file and writes a GROMACS NDX file for each QM region and for Link atoms.

Usage:

cp2kinput2ndxformat.py [options] cp2kinputfile

get_qm_kind.py

Reads a PDB containing the QM region and writes the atom indexes in the CP2K input format.

Usage:

python3 get_qm_kind [options] pdbfile