RE: AMBER: vdw of h atoms

From: Bill Ross <>
Date: Fri, 28 Oct 2005 17:21:56 -0700 (PDT)

> It is my understanding that the Aqvist parameters are designed to
> reproduce both the energy of solvation and the correct ion-water
> distance. While a continuum of parameters can reproduce one or the
> other, only one value of A and one of B reproduces both simultaneously.

It is my experience that multiple pairs of e,R* values can reproduce
ion-water first peak and free energy diffs between ions. I.e. the
only thing that determines energy of solvation for a monovalent cation
in a single-vdw water model like tip or spc is the water-ion distance.

        Ion-Induced Stabilization of the G-DNA Quadruplex: Free
        Energy Perturbation Studies. W.S. Ross and C.C. Hardin
        Journal of the American Chemical Society 116, 6070 (1994).

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Received on Sat Oct 29 2005 - 01:53:00 PDT
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