van der Waals Radius of Certain Atoms
saric at bph.ruhr-uni-bochum.de
Tue Jul 7 05:48:40 EST 1998
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%
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!
Lehrstuhl fuer Biophysik
Projektgruppe Theoretische Biophysik
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