Re: [AMBER] free energy of solvation of small molecules

From: Hannes Loeffler <>
Date: Tue, 17 Nov 2015 14:17:16 +0000


Have a look into tutorial A9 and see if that can work for you.
Alchemical transformations can be done both "absolute" (the definition
of "small molecule" may be a question here) and relative (usually such
that changes are small). In this context, you may want to look into the
work done by David Mobley, in particular FreeSolv (a database of
absolute free energies of quite a large number of "small"
organic molecules).


On Tue, 17 Nov 2015 15:51:50 +0200
Fabian gmail <> wrote:

> Hi,
> Is there a way in Amber to compute the free energy of solvation of a
> single small molecule, using a mixture of solvents?
> I know how to prepare the solvent mixture with packmol and the small
> molecule and peform the simulation, my question is about the
> calculation itself. I am interested to compare several different
> drugs in several different solvent mixtures.
> If somebody has done something similar and can give me some inputs or
> direct me some relevant papers I will much appreciate that.
> Thanks a lot,
> Fabian
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering Technion - Israel Institute of Technology, Haifa 32000,
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> _______________________________________________
> AMBER mailing list

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Received on Tue Nov 17 2015 - 06:30:03 PST
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