Well, you don't need GROMACS for that. You can use several tools for Binding Site Calculations (both protein-protein and protein-ligand type).

Follow the given URL to view the list of tools https://bip.weizmann.ac.il/toolbox/structure/binding.htm . However, once you compute the binding site, you can model the antigen interactions or dock the antigen and do a MD to analysis using GROMACS to analyse the stability of the binding.

You should conduct some research on the programme you want to utilise.

You can try gmx_qk based gmx_trj_qk tool to analyse trjectory analysis for contacts, distance and H-bond contacts at which time frame.

After knowing the exect frame you can extract them and analyse using any molecule viewer i.e., pymol or VMD.

Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...

Kangkon Saikia Thanks for the link you've provided, it really helps.

Harvinder Singh Ramin Ekhteiari Salmas Thank you for your answers, I'll try both ways.