Re: AMBER: HB dynamics in water and Ion solvation free energies

From: David A. Case <>
Date: Tue, 22 Jul 2003 19:18:51 -0700

On Tue, Jul 22, 2003, Ioana Cozmuta wrote:
> 2. What is the best way to estimate absolute free energies of hydration
> for a given ion (the way defined by Aqvist): Delphi, Gibbs, ...which
> module?

A really good reference is:

%A T. Darden
%A D. Pearlman
%A L.G. Pedersen
%T Ionic charging free energies: Spherical versus periodic boundary
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998

Use sander (thermodynamic integration section) to carry out similar

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Jul 23 2003 - 03:53:01 PDT
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