[gmx-users] force field for prodrg server
jalemkul at vt.edu
Wed Dec 4 16:39:17 CET 2013
On 12/4/13 10:24 AM, Mahboobeh Eslami wrote:
> hi dear Justin
> You've written the following context in your tutorial:
> Force field (GROMOS96.1/GROMOS87): "GROMOS96.1" refers to the first version of the GROMOS96 force field, 43A1. "GROMOS87" refers to the (outdated!) GROMOS87 force field. Choose "GROMOS96.1" to get 43A1 parameters for our ligand
> but I don't see the option for Select the force field in PRODRG server
PRODRG is now hosted by a company, so I don't know what sorts of changes they
have introduced. There is no more force field selection, so it's a black box, I
suppose. Given that you probably have to re-write the topology anyway, it
probably doesn't matter much except for a few atom types that may be different
between the force fields.
ATB is probably a better option; I think its output is generally much more
reliable than PRODRG. I'll probably revise the tutorial at some point, but the
use of PRODRG to get a flawed topology is a good teaching tool.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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