Protein-Protein simulation

User discussions
1

GROMACS version: 2018.8
GROMACS modification: Yes
Here post your question.
…
Hi,

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?

Regards

Nupur Nagar

2

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.

3

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

4

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.

5

Hi

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

6

Hi,
Thank you very much.
I have come across this:
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00251
But it also needs further improvements.