On 6/17/14, 11:26 PM, Timothy Click wrote:
Greetings from Taiwan. I am having a bit of trouble setting up a carbohydrate
in Gromacs. I have a PDB file that has a glucan chain between a graphene
bilayer, but when I run pdb2gmx, it complains of missing atoms. Yes, an
oxygen is supposed to be missing because of the 1,4 beta glycosyl linkage. I
want to use the CHARMM36 force field, which has the individual carbohydrate
defined. If I use CHARMM, I have no problem setting this up (initially setup
to use NAMD), but I prefer Gromacs.
Indeed, this is a known problem/limitation since CHARMM applies patches when
piecing together oligosaccharides. Gromacs doesn't do that. The only way (at
present) to do this entirely within Gromacs is to define your oligosaccharide as
its own residue in the .rtp file. I believe someone (Roland?) mentioned a
Python script that could patch things together, but that's the only workaround
that I know of.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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