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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
