[gmx-users] one protein and 4 ligands

[Justin Lemkul]

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

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

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