AMBER Archive (2008)

Subject: Re: AMBER: Bennett acceptance ratio with Amber10

From: steinbrt_at_scripps.edu
Date: Tue Aug 26 2008 - 08:45:55 CDT

Hi Samuel,

unfortunately, the Bennett acceptance ratio method is not implemented in
the Amber TI code at the moment. It is on the list of things to maybe be
put into it in the near future, though.

Kind Regards,

Thomas

>
> Hello, Amber users
>
> I would like to know if it is possible to use the Bennett acceptance ratio
> method with Amber 10 to calculate free energy differences? I'm aware about
> the theory behind the method but I would like to know how to set up the
> systems in Amber 10.
>
> I've started a project were I've calculated dG of some ligand-protein
> systems using TI and by using the scheme in the TI tutorial for Amber 10.
> Is it possible to use some data or the trajectories from these simulations
> when calculating the Bennett acceptance ratio? Is it gonna work with the
> soft-core potentials?
>
> Best regards,
> Samuel Genheden
> Lund university, Sweden
>

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