From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Mar 29 2012 - 00:58:54 CDT
look for "Huige and Altona" -> "Force Field Parameters for Sulfates and
Best if 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: Mittwoch, 28. März 2012 19:18
> An: Norman Geist; mkuttel_at_cs.uct.ac.za
> Cc: Namd Mailing List
> Betreff: Re: namd-l: Glycosaminoglycan sulfate group with CHARMM
> Hi Norman and Michelle,
> Thanks a lot for your replies, very useful answers.
> Dear Norman,
> I knew about GLYCAM FF and I have already used it for a heparin
> but in my group we want to use also CHARMM for carbohydrates and I
> would really appreciate
> if you could be more precise about the paper(s) you mentioned, where
> used CHARMM FF to model heparin (or a type of heparin derivative).
> Dear Michelle,
> With regard to your proposed 3 options:
> 1) I have already contacted MacKerell group and the conclusion is that
> they have not
> derived the parameters I am looking for yet.
> 2) The answer is (above) because we want to implement CHARMM FF too.
> 3) I think, as you pointed out, this is the best and quickest
> "temporary" solution to be
> adopted at the moment.
> Many thanks again.
> All the best,
> Il 23 marzo 2012 06:48, Norman Geist <norman.geist_at_uni-greifswald.de>
> ha scritto:
> > Hi Massimiliano,
> > 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
> > good papers out there aswell as from the GLYCAM FF. There's also a
> > that has full parameter set for amber and charm with
> > etc. If I remember right, the paper was about heparin. Also there are
> > interesting papers about the ring conformations within heparin.
> > Best of luck
> > Norman Geist.
> >> -----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
> >> and he/she can help
> >> me.
> >> 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,
> >> alpha and beta,
> >> C2 and C6), as described in
> >> "CHARMM Additive All-Atom Force Field for Phosphate and Sulfate
> >> to Carbohydrates"
> >> Sairam S. Mallajosyula, Olgun Guvench, Elizabeth Hatcher and
> >> 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
> >> mozz76_at_gmail.com
> >> maxp_at_iesl.forth.gr
> 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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