I would actually recommend glycam and ff99SB. 99SB has been shown now
in several studies to perform better than ff03, and in my opinion the
charge model is consistent with glycam while that in ff03 may not be.
I'm not sure if anyone has tried the combination of ff03 and glycam,
whereas ff99SB uses the ff94 charge model and there are many studies
of this combination.
On Thu, Nov 20, 2008 at 9:45 AM, Barbault Florent
<florent.barbault.univ-paris-diderot.fr> wrote:
> Hello,
>
> I think you should use glycam and ff03. This works pretty well. Glycam deals
> with carbohydrates efficiently. Biomacromolecules and water are included in
> ff03 along with some ions
> Hope this will help.
>
> Regards
> Florent
>
> Le jeudi 20 novembre 2008, Wang,Ying a écrit :
>> Hi, dear all,
>> if i want to simulate a system including glycoprotein, protein,
>> polysacchride and ions. which forcefiled should i use? gaff?
>> Thanks a lot!
>>
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>
>
>
> --
>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences
>
> NEW ADDRESS !!!
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://www.itodys.univ-paris7.fr/
> tel : (33) 01-57-27-88-50
> e-mail : florent.barbault.univ-paris-diderot.fr
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Received on Fri Dec 05 2008 - 16:09:51 PST
