AMBER Archive (2006)

Subject: AMBER: parm*.dat

From: Ivelin Georgiev (
Date: Thu Sep 28 2006 - 11:39:23 CDT

For the vdW energy computation, R* = R_i + R_j, is computed as the sum
of the vdW radii (read from the parm*.dat file) of the two atoms i and
j. Is this in contradiction to the claim that the combining rule used is
the arithmetic mean (see Table 13 in [1])?

[1] Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould,
Kenneth M. Merz, Jr., David M. Ferguson, David C. Spellmeyer, Thomas
Fox, James W. Caldwell, and Peter A. Kollman. "A Second Generation Force
Field for the Simulation of Proteins, Nucleic Acids, and Organic
Molecules." J. Am. Chem. Soc. 1995, 117, 5179-5197.
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