AMBER Archive (2000)

Subject: VdW numbers in Amber

From: Dow Hurst (dhurst_at_ksumail.kennesaw.edu)
Date: Wed Feb 02 2000 - 11:27:15 CST

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
Systems Support Specialist  Fax:    770-423-6744
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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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