AMBER Archive (2008)

Subject: Re: AMBER: AMBER forfield choose

From: Barbault Florent (florent.barbault_at_univ-paris-diderot.fr)
Date: Thu Nov 20 2008 - 10:21:17 CST

Hello,

In fact I did only carbohydrates-carbohdyrates interactions and I used ff03
only for water....

Regards
Florent

Le jeudi 20 novembre 2008, Carlos Simmerling a écrit :
> 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_at_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_at_univ-paris-diderot.fr
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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_at_univ-paris-diderot.fr
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