[gmx-developers] SASA / VDW radii

[David]

Hi,

is anyone aware of gromacs applications that rely on certain values of
the Van der Waals radii (in vdwradii.dat)?

The radii are read by the following programs:
gmxcheck
ngmx
editconf
genbox
g_sas

I have a new set of values from the msms program (scripps) with which we
can reproduce the areas calculated by msms with a different algorithm.
The differences in radii are quite small, but it would, e.g. give fewer
solvent molecules when running genbox, and obviously it would also give
different SASA. 

Values are:
Atom	OLD (gromacs)	MSMS
C     0.15		0.174
F     0.12		0.14
H     0.04		0.12
N     0.110		0.154
O     0.105		0.14
S     0.16		0.18

Do you think it is a problem to replace the old values by the ones from
MSMS?

-- 
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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