[gmx-users] Membrane protein and ligand simulation

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Fri May 17 17:15:08 CEST 2019

Dear All,

I am interested in carrying out a simulation of a membrane protein
(embedded in DPPC, already equilibrated and simulated) with a ligand
(having a net charge of 0).

I had carried out docking of the ligand with the protein (in this
conformation) and processed it through ATB server.

I wanted to know, which is the ideal step to incorporate the ligand.gro to
the system. I am assuming that it is better to do this before energy
minimization step.

I also feel that since we are adding a ligand to the box which is already
solvated. It might be a good option to remove equivalent number of SOL
molecules from the box.

For example, if the ligand has 30 atoms, should we remove 30 SOL molecules
from the box?

I am assuming this because, when we add ions, gmx replaces equivalent
number of SOL molecules with the ions. Should we be removing lipid
molecules from the box instead, as it is in the vicinity of the protein and
ligand? I  felt that, as the ligand is a small molecule and during the
course of simulation (production run), the lipid part might rearrange and
it would be sufficient if we remove the SOL molecules instead.

Can you please tell me, if there is a tool or option to remove excess
solvent/lipid molecules from the box.
Also, can we identify the specific lipid molecules that might be in the
location of the ligand using gmx? I do know that, this could be done using
vmd but, was curious if gmx has any in-built option to do this.

I would be grateful, if you can give your valuable opinion and inputs
regarding how to go about simulating a membrane protein with a ligand.
Thanks in advance.


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