[gmx-users] CHARMM36 force field available for GROMACS

[Justin Lemkul]

On 4/10/14, 2:51 AM, gsettanni wrote:
> Hi Justin and Roland,
>
> we are interested in simulating a glycosilated protein. We already have a
> pdb file  (and psf topology) with  the charmm/namd format/nomenclature. We
> managed to have pdb2gmx read the carbohydrate residues by adding the
> relative entries in the residuetypes.dat, however we have not yet been able
> to add the covalent bonds necessary to reproduce the correct branched
> carbohydrate chains. Is there any solution for that?
> Roland seems to have one, although suboptimal. would it be possible to share
> it?
>

Using specbond.dat might help, but often these types of patches will require 
modification of atom types depending on the linkage, so there isn't any solution 
completely within pdb2gmx that will suffice, outside of building a residue from 
the original PRES entries in the CHARMM files, which is what it sounds like 
Roland's program does.

-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 601
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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