hi,
you should first perform an umbrella sampling simulation, to slowly
eject your ligand from its binding site. Look at the manual for the
distance restrained MD. Then you have to post-process the
ligand-receptor distances with the WHAM procedure for example to get the
PMF.
This quite a difficult task to do, and the simulations have to be rather
long to get a correct sampling of the distance in each US window.
Good luck
Jerome
On Thu, 2007-05-03 at 17:46 +0800, Catein Catherine wrote:
> Dear Sir/Madam,
>
> 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?
>
> Best regards,
>
> Cat
>
> _________________________________________________________________
> Learn English via Shopping Game, FREE!
> http://www.linguaphonenet.com/BannerTrack.asp?EMSCode=MSN06-03ETFJ-0211E
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
--
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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 06 2007 - 06:07:18 PDT
