What are the VdW radii used in the Weiner et. al. force field?
Here are the carbon numbers I have found by looking in "Jeffrey and
Saenger, Hydrogen Bonding in Biological Structures, Springer-Verlag,
1991."
Pauling = 1.2 A
Bondi = 1.70 A
Allinger= 1.75 A
I have looked in Oxford Molecular's Chem-X program and they give:
MM2 = 1.60 A
Amber2.0 = 1.85 A
The ChemX numbers are actually scaled up CPK radii by a constant,
1.6667 A. The actual stored numbers for the CPK radii are:
MM2 = 0.96 A
Amber2.0 = 1.11 A
I am interested in what Amber is using in the united atom force field
for carbons and nitrogens. Also, do atom types have different radii
because of hybridization differences? It is interesting to me how the
force fields use a value appropriate for molecular mechanical
calculations while visualization programs seem to use an Xray
diffraction derived value for display. Thanks for the help,
Dow
PS. Please reply to the amber list serv, not just to me. Thanks!
--
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Dow Hurst Office: 770-499-3428
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Chemistry Department SC428 Email: dhurst_at_ksumail.kennesaw.edu
Kennesaw State University Dow.Hurst_at_mindspring.com
Kennesaw, GA 30144
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Received on Wed Feb 02 2000 - 09:27:15 PST
