AMBER Archive (2008)

Subject: RE: AMBER: Bennett acceptance ratio with Amber10

From: Samuel Genheden (a03samge) (a03samge_at_student.his.se)
Date: Wed Aug 27 2008 - 01:04:28 CDT

Hello, Thomas

Even if it is not implemented at the moment I guess I can implement some code by myself. However, I still would like to know if I can use the trajectories from my TI simulations, to get the values I need to compute the Bennett acceptance ratio. I'm not sure what information the mdcrd file contains for the V0 and V1 states, and if I can use some code of mine to calculate the potential energy along the trajectories, in order to compute the Bennett acceptance ratio. I would like you to tell me if it is possible from a theoretical point of view, sort to say.

Hope I made myself clear,
Kind regards,
Samuel

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of steinbrt_at_scripps.edu
Sent: Tue 8/26/2008 3:45 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Bennett acceptance ratio with Amber10
 
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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