[gmx-users] CHARMM36 and carbohydrates

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 13:47:15 CEST 2014

On 6/17/14, 11:26 PM, Timothy Click wrote:
> Greetings from Taiwan. I am having a bit of trouble setting up a carbohydrate
> in Gromacs. I have a PDB file that has a glucan chain between a graphene
> bilayer, but when I run pdb2gmx, it complains of missing atoms. Yes, an
> oxygen is supposed to be missing because of the 1,4 beta glycosyl linkage. I
> want to use the CHARMM36 force field, which has the individual carbohydrate
> defined. If I use CHARMM, I have no problem setting this up (initially setup
> to use NAMD), but I prefer Gromacs.

Indeed, this is a known problem/limitation since CHARMM applies patches when 
piecing together oligosaccharides.  Gromacs doesn't do that.  The only way (at 
present) to do this entirely within Gromacs is to define your oligosaccharide as 
its own residue in the .rtp file.  I believe someone (Roland?) mentioned a 
Python script that could patch things together, but that's the only workaround 
that I know of.



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


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