From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Mar 23 2012 - 01:48:05 CDT
we do also simulate heparin, controitin sulfate and hyaluronic acid. As far
as I know, we got the charges by qm and the forcefield parameters by some
good papers out there aswell as from the GLYCAM FF. There's also a paper
that has full parameter set for amber and charm with bonds,angles,torsions
etc. If I remember right, the paper was about heparin. Also there are
interesting papers about the ring conformations within heparin.
Best of luck
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Massimiliano Porrini
> Gesendet: Donnerstag, 22. März 2012 16:09
> An: Namd Mailing List
> Betreff: namd-l: Glycosaminoglycan sulfate group with CHARMM
> 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-
> 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 : M.Porrini_at_ed.ac.uk
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