[gmx-developers] SASA / VDW radii

David spoel at xray.bmc.uu.se
Mon Aug 16 12:20:36 CEST 2004


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:

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

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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