[gmx-users] Carbohydrate force fields in GROMACS

[Justin Lemkul]

On 3/20/15 12:30 PM, mish wrote:
> Many thanks.  I know parameters are available in literature but my question
> was how to use them in GROMACS. Now, I can see different residue names
> (e.g  AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM).
> I think I will need to edit input pdb file accordingly. However, I am still

Yes, .rtp and coordinate file residue names must match.

> not sure of methylated monosaccharides have to be constructed as "modified
> monosaccharides", or there are CHARMM parameters for methy (as  a separate
> residue) available and one should use 2 residues in such case. I will have
> a look in archive to find-out how to create  modified monosaccharides.
>

In CHARMM, there are "patches" that are applied to various residues.  There is 
limited support for such modifications in GROMACS.  You can define .tdb entries, 
but those only work for Protein, DNA, and RNA.  So you should not define 
separate residues for, e.g. a monosaccharide and a methyl "residue."  Instead, a 
methylated sugar as a single .rtp entry is the foolproof approach.  Chapter 5 of 
the manual is your friend (.rtp syntax is straightforward) as well as 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-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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