AMBER Archive (2004)

Subject: Re: AMBER: Sander TI

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 21 2004 - 10:15:50 CST

On Mon, Dec 20, 2004, Cai, Yufeng wrote:
>
> I am using Sander to perform TI calculating the differnce of free
> energy between a protein wildtype and mutant with an inhibitor. I am
> trying to decomposite the free energy by residues (or by atoms). Does
> anyone has any idea to do this in Sander? Thanks a lot.

I don't know of any such facility. Note two things: decompositions of free
energies into pieces are generally path-specific; with PME or GB models, the
energy is not pairwise decomposable, so that there is no rigorous result there
either.

But you still might learn some interesting things by accumulating the Delta-V
values in pieces; you would have to modify the codes to do this.

....good luck...dac

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