[gmx-users] Topology for Ligand from Prodrg server and force field 54a7 for protein

[Justin Lemkul]

On 5/27/15 11:06 PM, Vy Phan wrote:
> Dear Gromacs Users
> I use the force field 54a7 for protein. Can I simulate the protein-ligand
> complex with topology of ligand get from PRODRG server.
>

See my response to your glutathione question.  Don't use PRODRG topologies 
unless you correct all the problems in them.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================