van der Waals Radius of Certain Atoms

[Marc Saric]

Hi all,

I have a problem with the definition of van der Waals radii:

The problem: I want to extend a the amber94-library for the free
molecular modelling programm Molmol (Bruker & ETH Zuerich, R.Koradi),
especially Mg, Ca, Fe and other inorganic atoms are missing in the
standard library. The problem is, that I can´t find a consistens set of
vdW-Radii (i.e. the predefined numbers differ from what I got from
several tables (IUPAC- periodic-system published by
VCH-Verlagsgesellschaft for example). 

In general this is no big problem as these radii are only used for
display purposes, but I think the "size"-relations between different
atom-types should be saved, which means, one has to stick to a single
definition of vdW-radii.

In the amber94-lib published with Molmol, it is mentioned, that there is
apparently no common solution for this problem, and that vdW-Radii are
somewhat arbitrary choosen (i.e. defining the radius as 80% vdW or 100%
or whatever).

Is there any common definition of vdW-Radii or does someone know what to
use best for representation of atoms in modelling programs???

Thanks in advance!

-- 
Bye,


Marc Saric


Lehrstuhl fuer Biophysik
Projektgruppe Theoretische Biophysik
http://www.bph.ruhr-uni-bochum.de/

Ruhr-Universitaet Bochum
Germany