[gmx-users] one protein and 4 ligands
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.
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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