[gmx-users] Carbohydrate force fields in GROMACS

[Justin Lemkul]

On 3/20/15 11:51 AM, mish wrote:
> Dear all,
>
> I am very new to Gramacs (switching from AMBER in order to use GROMOS and
> CHARMM force fields for carbohydrates) and need some help in preparing
> topologies. I had a brief look in the tutorials and gromacs force field
> files but I could not find any useful information about using GROMOS or
> CHARMM force-field for monosaccharides. I would very happy of there are
> some tutorial where it is described. I had a deep look in the ff files and
> it loooks like parameters for carbohydrates are not included like for
> proteins (as it is done for GLYCAM in Amber). Can someone suggest me how to
> set-up a simulation of protein monosaccharides (Methyl-Mannose) using
> GROMOS and also CHARM. Moreover, what would be the appropriate choice for
> protein in both case ? Although, I would like to use AMBER for proteins.
>

We provide the full CHARMM36 force field, including all the monosaccharides:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

If you want to construct modified monosaccharides or polysaccharides, you have 
to create special residues in the .rtp for pdb2gmx to process them.  See 
previous discussions on this topic in the archive.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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