[gmx-users] N-acetyl-d-glucosamine parameters

Thomas Piggot t.piggot at soton.ac.uk
Tue Jan 18 11:10:26 CET 2011

You could use GLYCAM for the N-acetyl-d-glucosamine with an AMBER force 
field (probably 99SB or 99SB-ILDN) for the protein. I have never used 
GLYCAM parameters in GROMACS but I think it should be fairly easy to do 
using one of the ACPYPE or amb2gmx.pl tools.



Renato Freitas wrote:
> Hi all!
> I want to do a simulation of a protein that have a disaccharide
> (formed by two units of the N-acetyl-d-glucosamine) covalently bonded
> to the L-asparagine amido group of the protein.
> Is there an adequate force field in gromacs for dealing with
> N-acetyl-d-glucosamine?
> Any help would be appreciated,
> Thanks
> Renato

Dr Thomas Piggot
University of Southampton, UK.

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