[gmx-users]D Gsol from g_sas calculation

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 17 09:23:39 CEST 2008

limei zhang wrote:
> Hi to all,
> I did surface calculation on a protein either with or without 
> Cu-binding, using g_sas with exactly the same parameter setting. For the 
> delta solvation energy from the output file (the the 5th column in the 
> output file with a label of D Gsol), non-Cu bound protein gives all 0, 
> but the Cu-protein gives values from 0- 4 KJ/mol/nm^2. Could anyone tell 
> me how the delta solvation free energy is calculated?  Particularly, 
> what is the delta solvation free energy relative to?
The program spits out a reference to an Eisenberg paper. Please check 
the code as well. In my hands the results are close to useless.

> Thanks very much,
> Limei
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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