[gmx-users] glycosylated residues

Lars Meinhold lars.meinhold at iwr.uni-heidelberg.de
Fri Jan 13 21:26:32 CET 2006


I would like to perform MD on a protein which has
some residues glycosylated:

N-glycosylated ASN (Asparagine)
O-glycosylated SER (Serine)     
               THR (Threonine)

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.

More information about the gromacs.org_gmx-users mailing list