From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Wed Mar 28 2012 - 12:18:08 CDT
Hi Norman and Michelle,
Thanks a lot for your replies, very useful answers.
I knew about GLYCAM FF and I have already used it for a heparin derivative,
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 they
used CHARMM FF to model heparin (or a type of heparin derivative).
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>
> 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 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
> 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 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
-- 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
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