[gmx-users] one protein and 4 ligands

Justin Lemkul jalemkul at vt.edu
Sun Dec 3 23:28:02 CET 2017

On 12/2/17 3:20 PM, Mahboobeh Eslami wrote:
> I want to do MD simulation on a protein-ligand complex. the protein includes 4 chains and the ligands are ASP amino acid. I want to use Amber topologies from acpype for generating necessary files for ligands. please guide me to do this work correctly.  Can I use GMXPBSA script to obtain free energy value for the studied protein-ligand

Your situation is functionally no different than any protein-ligand 
complex. Are you having a specific problem? There are plenty of 
tutorials and mailing list posts from which you can learn.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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