[gmx-users] g_sas, what's it all about?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 30 12:58:38 CEST 2008
Peyman Yamin wrote:
> Hello List!
> I use g_sas to calculate the solvent accessible surface area of some
> amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if the
> hydrophilic part is somehow not recognized, or these terms mean different
> things in g_sas context? For Triton, for instance, a big surface is
> hydrophilic, to my knowledge!
xmgrace -nxy sas.xvg
> I use ffG43a1. Is it a strange behavior to calculate SAS from a UA trajectory?
> How is the DGsolv calculated by g_sas? and the areas ? which algorithm? where
> is the code?
> Is there any program with which one could calculate the volume enclosed by SAS
> resulted from g_sas?
> I see different posts in the mailing list addressing the accuracy of g_sas!
> Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?
> Any comment is truthfully appreciated :)
> P.S. Edmund Husserl believed, that we would indeed be in a nasty position, if
> empirical science were the only kind of science possible.
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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