Glycosaminoglycan sulfate group with CHARMM

From: Massimiliano Porrini (
Date: Thu Mar 22 2012 - 10:09:03 CDT

Dear all,

I know that the following issue is not properly related to NAMD
mailing list and I apologize
for that, but probably some NAMD's user has already gone through this
and he/she can help

I am trying to simulate a glycosaminoglycan (GAG) with CHARMM36 all-atom
carbohydrate force filed (FF).

If I understood well, the sulfate group of the above FF was modeled
only when attached
to several carbon atoms of the sugars (like for instance the C1, both
alpha and beta,
C2 and C6), as described in

"CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked
to Carbohydrates"
Sairam S. Mallajosyula, Olgun Guvench, Elizabeth Hatcher and Alexander
D. MacKerell, Jr.
Journal of Chemical Theory and Computation, 8, 759-776 (2012).

But GAGs and heparin derivatives have the sulfate groups attached
also to nitrogen atoms.

Any idea or hint on how to model this specific sulfate group would
really appreciated.

Thanks a lot in advance and all the best,

Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails :

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