[gmx-users] OPLS-2005 forcefield parameters for carbohydrates in Gromacs 4.0.7?

Steven R. Kirk stevenrkirk at gmail.com
Mon Jul 12 21:07:12 CEST 2010


I'm using Gromacs 4.0.7, and I'm looking for the OPLS-2005 all-atom
forcefield, which I'm told contains parameters and residue topologies
that will allow me to model beta (1-4) cellobiose.

Does the standard OPLS-AA parameter set supplied with Gromacs 4.0.7
contain the OPLS-2005 parameters for carbohydrates (the files are
labelled '2001 amino acid dihedrals') ?

If so, can anyone tell me what the correct residue names are for use
with cellobiose?

If not, does anyone have these parameter files so I can just drop them
into GMXRC?

I have searched the wiki, the mailing list, and the web, but haven't
found anything so far. I have found a couple of papers by Kony et al.
describing the use of something called OPLS-AA-SEI for carbohydrates,
but again, no actual forcefield data.

I would be grateful for any help.
Many thanks in advance,

Steve Kirk

Prof. Steven R. Kirk
College of Chemistry and Chemical Engineering
Hunan Normal University
Changsha 40081
Hunan Province, China

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