[gmx-users] Build oligosaccharide topology with pdb2gmx

[Justin Lemkul]

On 3/4/15 7:54 AM, Elena Lilkova wrote:
> Dear GMX community,
>
> I would like to use the CHARMM 36 carbohydrate force field to simulate an
> oligosaccharide. I read the pdb2gmx section of the manual, but I am still
> wondering how to build the topology for my oligosaccharide.
>
> My first question is can I add in the "residuetypes.dat" residues that are
> neither protein, nor DNA, RNA, water, or ions, but say type sugar.
>

Listing it simply as "Other" is the straightforward solution.

> Next, how can I link the individual saccharides. I would like to use two
> of the several linkages, that are parameterized in the force field (i.e.
> PRES 14aa and PRES 14ab). This means that in both of the two consecutive
> saccharides some atoms should be deleted and some partial charges should
> be changed.
> I now how to do this with the psfgen plugin of vmd, but how am I supposed
> to achieve this with pdb2gmx. I should probably make a termini database
> file and a special bonds file, right?
>

No, the .tdb will only affect the terminal residues and won't do internal 
patching.  At present, there's no built-in way for pdb2gmx to do patching like 
CHARMM does.

The possible solutions are:

1. Write a script to convert the PSF to GROMACS .top format (eventually we will 
support PSF natively)
2. Create an .rtp entry for the fully built oligosaccharide, with all of the 
changes to atom types and charges already made.  The oligo effictively becomes 
on single "residue."

-Justin

-- 
==================================================

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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