Re: [AMBER] non-bonding parameters

From: Jason Swails <>
Date: Fri, 19 Nov 2010 20:03:38 -0500

The vdw.pdf file shows the relationships between sigma and r0. If notation
is consistent, r0 = 2^(1/6)*sigma. So if the stotes parameters list a sigma
and an epsilon, I'd use the epsilon as-is (converted to kcal/mol if it's not
already there) and adjust the sigma according to the above equation, with
the result in Angstrom. But again, the paper should probably be explicit
about which parameters in whatever equation they are talking about.

Good luck!

On Fri, Nov 19, 2010 at 7:32 PM, Bill Ross <> wrote:

> R* is not sigma to my belief.
> Maybe sigma is where the potential is at 0, while definitely R* is
> the minimum energy point.
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Nov 19 2010 - 17:30:03 PST
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