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

From: David A. Case <case.scripps.edu>
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
conditions
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998


Use sander (thermodynamic integration section) to carry out similar
simulations.

...good luck...dac 

-- 
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David A. Case                     |  e-mail:      case.scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Jul 23 2003 - 03:53:01 PDT
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