[gmx-users] CHARMM36 force field available for GROMACS

Justin Lemkul jalemkul at vt.edu
Wed Oct 9 20:02:56 CEST 2013

On 10/9/13 1:26 PM, Roland Schulz wrote:
> Hi Justin,
> are you guys planning anything to make pdb2gmx understand the CHARMM patch
> residues? We have some python scripts which generate new residues based on
> the patch residues, which allows us to simulate branched molecules (e.g.
> glycosylation or lignin). But that approach is very suboptimal and I think
> a more general approach would be very nice.

It's something we're thinking about, though not something we have a generalized 
solution for at the moment.  For example, in CHARMM we generate all nucleic 
acids as RNA and then patch the 2' site to become DNA.  Because of this 
procedure, we had to hard-code the DNA .rtp entries so that they could be used 
in GROMACS since there are no DNA entries in the top files.  It is just a 
microcosm of the larger patching architecture that would definitely be useful 
for polysaccharides and more complex chemical species.



Justin A. Lemkul, Ph.D.
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


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