[gmx-developers] SASA / VDW radii

Berk Hess gmx3 at hotmail.com
Tue Aug 17 12:11:20 CEST 2004

>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...

I agree.
But there are two different types a radii.
One for checking overlap (genbox, gmxcheck)
And one for generating surfaces (g_sas and probably editconf)

I guess we could keep vdwradii.dat the same.
And we could make files like vdwradii_msms.dat
and vdwradii_???.dat (where we need a name for the current g_sas set).
And add vdwradii_user.dat so the user can use his own radii.
g_sas, and maybe editconf, can then have a enum
???, msms, user that selects one of these files.


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