AMBER Archive (2004)

Subject: Re: AMBER: General Question about AMBER's Free Energy Perturbation Method

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 17 2004 - 17:26:34 CST

On Fri, Dec 17, 2004, Ilyas Yildirim wrote:
>
> Is there any sander tutorial which uses the TI Method? (Or any paper which
> uses the TI Integration method to calculate the Free Energy Difference of
> two structures)

Look at this:

%A T. Simonson
%A J. Carlsson
%A D.A. Case
%T Proton binding to proteins: pKa calculations with explicit and implicit
%solvent models
%J J. Am. Chem. Soc.
%V 126
%P 4167-4180
%D 2004

...dac

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