[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,
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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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