How can I use ProLIF to analyse protein-ligand interactions in Gromacs MD?

[nachotu]

Hello everyone, I'd like to use ProLIF to make a protein-ligand fingerprint from a gromacs MD simulation. Someone could help me?
Thank you all!

[cbouy]

Hi @nachotu ,

Have you had a look at the quickstart tutorial?
In the first cell at the beginning:

import MDAnalysis as mda
import prolif as plf
# load trajectory
u = mda.Universe(plf.datafiles.TOP, plf.datafiles.TRAJ)
# create selections for the ligand and protein
lig = u.atoms.select_atoms("resname LIG")
prot = u.atoms.select_atoms("protein")

just replace plf.datafiles.TOP with a path to your Gromacs topology, and plf.datafiles.TRAJ with a path to your trajectory.

MDAnalysis (which is used for reading the inputs) supports a wide range of formats including those from Gromacs so it should work out of the box.