[gmx-users] g_sas, VdW radii

[David]

On Thu, 2004-07-08 at 18:26, Michael Brunsteiner wrote:
> dear all,
> 
> Just tried to calculate the solvent accessible surface
> area for a structure including non-protein molecules.
> (using an extended OPLSAA FF, all atoms, however, are some
> OPLSAA type)
> 
> g_sas says: 
> WARNING: could not find a Van der Waals radius for 728 atoms
> 
> Does that mean 
> a) these atoms are not included in the calculation of the SASA, or
> b) some default value is used for these atoms ?
b) 0.14 nm (see src/gmxlib/atomprop.c)


-- 
David.
________________________________________________________________________
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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