[gmx-users] charmm topology for unknown residues in GMX

[Justin Lemkul]

On 9/5/14, 7:04 AM, xy21hb wrote:
> Dear all,
>
>
> I need to build up an unknown ligand in CHARMM force field in GMX,
> I understand PRODRG is a very decent choice, however, it only has a GMX force field.
> Is there any way I can build up a CHARMM topology for the use in GMX, or convert the PRODRG GMX topology into GMX CHARMM format?
>

The output of PRODRG is a Gromos96 topology, so no, you cannot simply convert it 
to become compatible with CHARMM.  You need to generate a CHARMM topology.  You 
can do that on www.paramchem.org; we provide conversion scripts to write Gromacs 
topologies from the CHARMM topology that it generates.

-Justin

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

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

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
http://mackerell.umaryland.edu/~jalemkul

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