[gmx-developers] SASA / VDW radii

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 17 12:01:50 CEST 2004

On Tue, 2004-08-17 at 10:27, Berk Hess wrote:
> Hi,
> >Do you think it is a problem to replace the old values by the ones from
> >MSMS?
> Replacing doesn't help as g_sas uses hardcoded radii.
> But since there are hardcoded we could have different sets of radii
> implemented. You could add the MSMS ones and make an enum
> option that selects the different sets.
> But maybe it would also be useful if the user could additionally
> set the radii himself?

Actually such number should not be hardcoded at all. We can have
different files with radii and have a flag to g_sas to use msms radii,
and by default use the old ones. Obviously it is kind of weird to have
genbox, gmxcheck etc. all use different radii...
> Berk.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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