From: Michelle Kuttel (mkuttel_at_cs.uct.ac.za)
Date: Fri Mar 23 2012 - 02:20:29 CDT
If the parameters aren't there yet, you basically have three options:
1. Wait for them to be added. This new force field is updating very regularly - I would email the MacKerell group to find out the ETA for the parameters your require.
2. Use another force field that has the suitable parameters - I am not aware of any that do, but I have not used GLYCAM series of force fields for AMBER , or
OPLS-AA  or the GROMOS 45a4 force field  - one of these may have suitable parameters.
3. Edit the topology and parameters files to "create" your own parameters by adding a sulfate-nitrogen bond and the corresponding angle and dihedral angle terms. This is a "hack", but can be a useful interim step, if you choose the parameters from suitable analogous bonds/angles/dihedrals (I would look at the protein force field).
1. Kirschner, K.; Yongye, A.; Tschampel, S.; Gonzalez-Outeirino, J.; Daniels, C.; Foley, B.; Woods, R. GLYCAM06: A generalizable biomolecular force field for carbohydrates. J. Comput. Chem. 2008, 29, 622-655.
2. Kony, D.; Damm, W.; Stoll, S.; van Gunsteren, W. F. An improved OPLSAA force field for carbohydrates. J. Comput. Chem. 2002, 23(15), 1416-1429.
3. Lins, R. D.; Hünenberger, P. H. A new GROMOS force field for hexopyranose-based carbohydrates. J. Comput. Chem. 2005, 26(13), 1400- 1412.
Michelle Kuttel, Ph.D.
Department of Computer Science
University of Cape Town
PH: +27 21 6505107
On 22 Mar 2012, at 5:09 PM, Massimiliano Porrini wrote:
> 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 : M.Porrini_at_ed.ac.uk
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