Re: [AMBER] Accuracy of solvation free energy calculated by 3D-RISM

From: David A Case <>
Date: Fri, 31 Jan 2014 08:09:10 -0500

On Fri, Jan 31, 2014, wrote:
> I'm calculating the solvation free energy by rism3d.snglpnt in Ambertool 12.
> I'd like to ask about the accuracy of the predicted solvation free
> energy (rism_exchem).
> For example, the calculated solvation free energy of ethanol is +7.4
> kcal/mol (closure=kh, water=tip3p), whereas the reported experimental
> value is -5.01 kcal/mol.

All hydration energies from 3D-RISM are too positive, but by a systematic
amount. This appears to be related to the high internal pressure the theory
predicts for water at its experimental density: it is too hard to make the
cavity into which the solute molecule must fit.

> And it has been shown that the uncorrected 3D-RISM approaches are not
> able to provide quantitative description of hydration (J. Phys. Chem. B,
> 2011, 115 (19), pp 6011–6022).

There are lots of discussions of this point, and corrections are available,
including in the paper you cited. See also:

%A D.S. Palmer
%A A.E. Frolov
%A K.E. Ratkova
%A M.V. Fedorov
%T Towards a universal method for calculating hydration free energies: a 3D
reference interaction site model with partial molar volume correction
%J J. Phys. Condens. Matter
%V 22
%P 492101
%D 2010

[There is another paper by J.-F. Truchon et al. that should appear soon in
JCTC addressing this issue.]

The Amber output provides the computed partial molar volume, so you can apply
the correction cited above yourself. I think(?) the next version of
AmberTools will directly report some of these "corrected" values.

Note that the electrostatic component of the hydration free energies appears
to be rather good, so that there are many applications of RISM (aside from
just looking at total hydration free energies) that do not require such

%A T. Luchko
%A I.S. Joung
%A D.A. Case
%T Integral equation theory of biomolecules and electrolytes
%B Innovations in Biomolecular Modeling and Simulation, Volume 1
%E T. Schlick
%C London
%I Royal Society of Chemistry
%D 2012
%P 51-86

[There is another paper by J.-F. Truchon et al. that should appear soon in
JCTC addressing this issue.]

...hope this helps....dac

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Received on Fri Jan 31 2014 - 05:30:02 PST
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