Interaction between protein(residues) and the ligand

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@jalemkul @avilla @alevilla

GROMACS version: 2.22.2
GROMACS modification: No

Hello forum members,

I have successfully completed the Protein-Ligand MD simulation by following the tutorial(by Justin Lemkul).
Now the challenge is to find which residues of protein are interacting with the Ligand. I tried to find such type of interaction by replicating Protein-Protein interaction protocol. First I made groups (ligand, res_1, res_2, res_3,…) in the index.ndx and in interaction.mdp. then I executed the following scripts (same as what I do to analyze protein-protein interaction)

"gmx grompp -f interaction.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o interaction_individual.tpr"
"gmx mdrun -v -deffnm interaction_individual -rerun pro1_*.trr -ntmpi 32"
"gmx energy -f interaction_individual.edr -o interaction_individual.xvg"

but didn’ t get any option to analyze. console doesn’t show the groups to choose the pairs and see the interactions.

My query is:
Is it possible to analyze such type of interactions? if so how to do it? Which command do I need to execute?

Thanks