Documentation for the HOLE: 5.0 van der Waals radii files
Copyright 1997 by Oliver S. Smart
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5.0 van der Waals radii files
At present five sets of van der Waals radii are supplied with HOLE (in separate
files). The files are supplied in the directory ~/hole2/rad.
The choice of which to use is made by a radius
card.
- amberuni.rad: uses the van der Waals radii given by Weiner et al. (1984), J.
Am. Chem. Soc. 106:765-768, which form part of the AMBER united atom
potential energy function. United atom carbon atoms (those to which
carbons are attached) are given different values.
- simple.rad: uses amber vdw radii but ignores united atom values. This is the
file which I use and it allows comparison to the results of Smart,
Goodfellow and Wallace (1993).
- bondi.rad: uses vdw radii specified by Bondi (1964) J. Phys. Chem. 68:441-451.
These are the "classic" van der Waals radii a fair bit shorter than those
used in amber.
- hardcore.rad: This contains "hard core" radii given by Turano, Pear and Busath
(1992) Biophys. J., 63:152-161. These radii are reduced variant of vdW
radii which give some kind of implicit representation of thermal motion.
- xplor.rad: This file has been kindly provided by Dr Ian Kerr,
Molecular Biophysics, Oxford University and contains radii derived
from XPLOR parameter file param19x.pro.
When reporting the results of hole don't forget to specify which set is used (to
allow comparison between works). If the you would prefer some other set of
radii please make a .rad file (amberuni.rad explains the format) and
send it to me
so that others can benefit.
Navigation:
- Back to contents
- Back to previous section 4.0 Sample input file
- On to next section 6.0 Visualization of HOLE results