Subject: Re: CCL:van der Waals radii for amino acids

From: [email-masked] (Eberhard von Kitzing)
Date: Fri, 27 Jun 1997 17:30:20 +0200

Dear Prof. Shapiro,

At 16:01 Uhr 24.06.1997, Hr. Dr. S. Shapiro wrote:
>        For a calculation I wish to perform, I require the van der Waals
>radii of each of the atoms (including hydrogen) in the 20 common amino
>acids.  If anyone can recommend a published source of this information (or
>if anyone should happen to have this information as an e-mailable file),
>I would appreciate hearing from you.

Of course the list of relevant articles is very long. Below please consider
a small subset.

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Misako Aida, Giorgina Corongiu and Enrico Clementi (1992). "Ab Initio force
fields for simulations of proteins and nucleic acids." International
Journal of Quantum Chemistry 42 1353-1381.

W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, et al.
(1995). "A 2nd generation force-field for the simulation of proteins,
nucleic-acids, and organic-molecules." Journal of the American Chemical
Society 117(19) 5179-5197.

T. P. Creamer and G. D. Rose (1995). "Simple force-field for study of
peptide and protein conformational properties." Methods in Enzymology 259
576-589.

P. Derreumaux and G. Vergoten (1995). "A new spectroscopic molecular
mechanics force-field - parameters for proteins." Journal of Chemical
Physics 102(21) 8586-8605.

David M. Ferguson and Peter A. Kollman (1991). "Can the Lennard-Jones 6-12
Function Replace the 10-12 Form in Molecular Mechanics Calculations."
Journal of Computational Chemistry 12(5) 620-626.

Thomas A. Halgren (1992). "Representation of van der Waals (vdW)
Interactions in Molecular Mechanics Force Fields: Potential Form,
Combination Rules, and vdW Parameters." Journal of the American Chemical
Society 114 7827-7843.

T. A. Halgren (1996). "Merck molecular-force field .2. mmff94 van-der-waals
and electrostatic parameters for intermolecular interactions." Journal of
Computational Chemistry 17(5-6) 520-552.

M.J. Hwang, T. Stockfisch, M. Hassan, D. Nguyen and A.T. Hagler (1993).
"Class-ii force-fields for peptides and proteins ." Biophysical Journal
64(N2) A  12-12.

William L. Jorgensen and Julian Tirado-Rives (1988). "The OPLS Potential
Functions for Proteins. Energy Minimizations for Crystalls of Cyclic
Peptides and Crambin." Journal of the American Chemical Society 110(6)
1657.

M. Kroeker and H. J. Lindner (1996). "The pimm force-field - recent
developments." Journal of Molecular Modeling 2(9) 376-378.

Jenn-Huei Lii and Norman L. Allinger (1991). "The MM3 Force Field for
Amides, Polypeptides and Proteins." Journal of Computational Chemistry
12(2) 186-199.

G. Luiti and F. Pirani (1985). "Regularities in van-der-Waals forces:
Correlations between the potential parameters and polarizability." Chemical
Physics Letters 122(3) 245-250.

K. T. No, O. Y. Kwon, S. Y. Kim, K. H. Cho, C. N. Yoon, Y. K. Kang, K. D.
Gibson, M. S. Jhon and H. A. Scheraga (1995). "Determination of nonbonded
potential parameters for peptides." Journal of Physical Chemistry 99(34)
13019-13027.

A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III and W. M.
Skiff (1992). "UFF, a Full periodic tabel Force Field for molecular
mechanics and molecular dynamics simulation." Journal of the American
Chemical Society 114 10024-10035.

Scott J. Weiner, Peter A. Kollman, David A. Case, U. Chandra Singh,
Caterina Ghio, Giuliano Alagona, Savatore Jr. Profeta and Paul Weiner
(1984). "A New Force Field for Molecular Mechanical Simulation of Nucleic
Acids and Proteins." Journal of the American Chemical Society 106 765-784.

======================================================================

Eberhard von Kitzing

Max-Planck-Institut fuer Medizinische Forschung
Jahnstr. 29
D 69115 Heidelberg
Germanny

email: [email-masked]
WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html