Intermolecular interaction for Absolute binding free energy

GROMACS version:2023.2
GROMACS modification: No

I need to run a ABFE and need help in defining intermolecular interaction section atoms and parameters.

We can’t provide help without more details.

I am trying to follow the tutorial provided here Absolute Binding Free Energy - Gromacs 2016 - AlchemistryWiki and for my protein-ligand complex how can I derive the intermolecular_interactions section mentioned in the top file of the tutorial along with parameters associated with it.

In the intermolecular interactions section you supply global atom numbers. Otherwise everything is the same as with intramolecular interactions.

Thanks for the reply.

I wanted to understand how to pick 3 atoms on protein and 3 atoms on ligand for this intramolecular interactions section.