af2cv

Python script to convert Alphafold output to collective variable

Usage:

python af2cv.py model.gro model.pkl > plumed.dat

model.gro - Gromacs file with the same atoms and atom numbers as in the simulation. Make sure that C-alpha atoms are labeled "CA".

model.pkl - Alphafold output pickle file. Amino acid sequence of the alphafold and Gromacs input must be the same.

Requirements:

• python3
• pickle
• numpy

Necessary postprocessing

• set the number of atoms in WHOLEMOLECULE to the number of atoms in the protein (default all atoms in model.gro)
• set up metadynamics or other enhanced sampling method according to Plumed documentation
• set epsilon if necessary (default no epsilon)
• set lambda (default 1000)