[gmx-users] g_sas dG
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 19 13:14:57 CEST 2014
On 2014-08-19 11:30, xy21hb wrote:
> Dear all,
> I just wanna calculate the SAS of a protein (ubiquitin) in a protein-in-water binary system,
> when I use g_sas, it asks me for a caculation group and output group,
> I chose the whole protein as both groups.
> However, the solvation free energy (dG) is positive and a bit large, ~ +300 KJ/mol,
> I would imagine solvating a protein, in general, should stabilize the protein.
> Is that true and how accurate is the dG compared to that from other methods lsuch as thermal integration, ...?
Do not trust these results at face value. Besides the model being very
crude to begin with, the implementation needs checking as well. It might
just be the sign though, you can compare the values in the data file
(dgsolv.dat IIRC) to the paper to begin with.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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