AMBER Archive (2006)

Subject: Re: AMBER: parm*.dat

From: Jianhui (
Date: Thu Sep 28 2006 - 16:24:49 CDT

Hello Ivelin,

Actually there is no contradiction. R*=(R_i + R_j)/2 while the distance in the VDW energy calculation is 2 times of R*. Because when calculate the energy, the distance is from the center of one atom to the center of the other atom, so it's two times of R*.

Best regards,
======= At 2006-09-28, 12:39:23 you wrote: =======

>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.
>The AMBER Mail Reflector
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