Protein-Protein simulation

GROMACS version: 2018.8
GROMACS modification: Yes
Here post your question.


I want to run an MD simulation for a docked protein-protein complex using the OPLS force field and doubt the process.

  1. Since it is a protein-protein complex, can I follow the ‘protein-ligand’ MD tutorial by Prof. Justin Lemkul?
  2. The protein used as the ligand is a multiepitope vaccine and is very big. So, how to develop a ligand topology for the protein? Also, which topology builder is good for doing so?


Nupur Nagar

Generate the entire topology with pdb2gmx. You have two proteins, nothing more. The second protein is not a “ligand” in the typical sense, which refers to some arbitrary species that is not covered by the force field. Never generate a protein topology with a general force field.

What is best force field to simulate the protein-protein complexes?

An honest but unsatisfying answer: there is no answer to this question in a general sense. If you find (by studying the literature) that a certain force field models a specific behavior that is relevant in your system very well, use that one.


Thank a lot for the suggestion. As per your recommendation, I have changed the force field too.

Thank you very much.
I have come across this:
But it also needs further improvements.