Hi,
just take care of the consistency between the description of your enzyme
an the description of your ligand... especially if you want to use GAFF
for the inhibitor.
I would recommend ff99SB since I don't think that ff03/GAFF
compatibility has been extensively studied. Or maybe I missed it !
Best
Jerome
Le jeudi 22 novembre 2007 à 10:20 -0500, Adrian Roitberg a écrit :
> Patel,
> Neither of those !
>
> See previous threads on this subject on the amber archives, but I
> strongly suggest either ff99SB or ff03.
>
> a.
>
>
> Patel, Bhavesh H wrote:
> > Hi all,
> >
> > I'm going to be running simulations on the interactions within a enzyme-inhibitor complex and I was wondering which amber force field, FF94 or FF99 would be best to use?
> > I know that FF94 is more helical friendly and that ther are some issues with FF99, for example, it can give an inaccurate description of electrostatic interaction between monomers at close distances of approach.
> > Any information will be much appreciated!
> > Thanks
> >
> > Bhavesh
> >
>
--
Jerome Golebiowski, PhD
LCMBA, team Chemometrics and Molecular Modeling
University of Nice, parc Valrose
06108 Nice Cedex2 France
tel : +33 (0)4 92 07 61 03
http://www.unice.fr/lcmba
http://www.unice.fr/lcmba/golebiowski
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Received on Sun Nov 25 2007 - 06:07:23 PST
