Protein-Protein simulation where one protein is a trimer

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1

GROMACS version: 2023.2
GROMACS modification: No
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Good day!

I would like to simulate a protein-protein system involving a death receptor-death ligand system. Death receptors typically trimerize when they recognize the approach of a death ligand. I ran one MD simulation and found that in the output file, only a monomer and the ligand was simulated and not the whole trimer. I followed the protein-ligand tutorial by Mr. Justin A. Lemkul, Ph.D. I was wondering if there is a way to simulate the whole trimer + ligand or would the output be just the monomer + ligand if the individual monomers that make up the trimer have the same sequence of amino acids.

I really appreciate any input in this. Thank you in advance!

2

The output of the simulation is based on whatever the input is. Simulate a monomer, get a monomer. Simulate a trimer, get a trimer.

Note that the protein-ligand tutorial is designed for non-protein ligands. You should not follow its protocol for a protein that is a binding partner/ligand. pdb2gmx can handle writing the entire topology for a multi-chain system.