[gmx-users] glycosylated residues
lars.meinhold at iwr.uni-heidelberg.de
Mon Jan 16 14:53:30 CET 2006
I would like to perform MD on a protein which has
some residues glycosylated (sugar added to amino acid):
N-glycosylated ASN (Asparagine)
O-glycosylated SER (Serine)
However, I could not find any force-field parameters
for the sugars in the gromacs package. I found parameters
for a sugar (NAG - acetylglucosamine) using PRODRG.
Can I easily bind the amino-acid and this sugar?
Which parameters should I use for the bonds?
e.g., for the ASN-NAG I'm stuck with the following bond:
H to sp3 carbon
to a 'HCOH'group - N - C - to a '-O-C' oxygen
Can anyone suggest a solution?
Thanks a lot, Lars.
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