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.
Cheers
Tom
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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