David Mobley is right, PMF can only give you a binding (or unbinding)
free energy.
In the manual, I think you can get the URL where WHAM is available, I
don't the URL anymore.
Good luck.
J
On Fri, 2007-05-04 at 10:13 +0800, Catein Catherine wrote:
> Dear David and Jerome,
>
> Thank you very much for your help! Could you mind to let me know how to do
> the WHAM, is it a module of AMBER, or another software?
>
> Cat
>
>
> >From: "David Mobley" <dmobley.gmail.com>
> >Reply-To: amber.scripps.edu
> >To: amber.scripps.edu
> >Subject: Re: AMBER: Potential of mean force, how to calculate rate of
> >dissociation?
> >Date: Thu, 3 May 2007 15:17:31 -0700
> >
> >Hi,
> >
> >>Could you please kindly help me? Can I do the potential of mean force
> >>calculation with AMBER? Can I calculate the rate of dissociation of a
> >>drug
> >>from the binding site? If yes, could you mind to give me some hints how
> >>to
> >>do so with AMBER?
> >
> >The other user who answered your mail is on the right track.
> >
> >But I should also point out that a potential of mean force will not
> >give you a dissociation rate. It will give you an equilibrium
> >dissociation constant (or a dissociation free energy, which is
> >related). If you want a dissociation rate, you'll have to look
> >elsewhere (experiment?).
> >
> >David
> >
> >
> >>Best regards,
> >>
> >>Cat
> >>
> >>_________________________________________________________________
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--
Jerome Golebiowski, PhD
Lab. Chemistry of Bioactive Molecules and Aromas,
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 May 06 2007 - 06:07:26 PDT
