Proteins Complex with Multiple Chains intermolecular interactions study

User discussions
1

GROMACS version: 2022.4
GROMACS modification: No

hello. I’m gromacs newbie and i woud like to do conduct the Molecular Dynamics Simulation for protein-protein complex which contains something about 16 protein chains (of 4 peptides). In my simulation I would like to recive and study the interaction energy between these peptides. how could i manage this in Gromacs? i’ve tried to find some tutorials on internet but i only found ones for protein-ligand compexes.

Thanks in advance :))))

2

Calculating interaction energy between any species is carried out the same way, it doesn’t matter if it’s two proteins or a protein and a ligand.

3

Thanks for your answer <3
But I have to ask one more question. Do you know any tools to use to estimate the intermolecular interaction energy of individual amino acid residues at the peptide binding sites after MD simulation?

4

Define each residue of interest as its own group in energygrps and compute the interaction energy. You can do this with any subset of atoms.