From owner-chemistry@ccl.net Fri Jun 15 14:06:00 2007
From: "David A. Case case ~ scripps.edu" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL: Problems about AMBER
Message-Id: <-34499-070613170007-2622-8MtSGoS+eigd+zJ5jcvGYQ_-_server.ccl.net>
X-Original-From: "David A. Case" <case..scripps.edu>
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Date: Wed, 13 Jun 2007 13:59:44 -0700
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Sent to CCL by: "David A. Case" [case(_)scripps.edu]

On Wed, Jun 13, 2007, littlecan p9894105%x%mail.ncku.edu.tw wrote:
>  
> Recently, I started using AMBER and have encountered problems regarding van
> der waals energy calculation.

It is far better to submit Amber-related questions to the Amber mailing list; 
see http://amber.scripps.edu for information on how to subscribe and post.

> We are not sure about either our calculation is incorrect or it is
> reasonable to have positive van der waals energy in those cases.

There is nothing intrinsically suprising about have a postive value here.

> 
> 2.                  In the 1995 paper by Cornell et al., the scale factor of
> 1/2.0 is recommended for reducing the 1-4 VDW interactions as used
> previously by Weiner et al. (lines 6 to 8 from the bottom of the right-hand
> column in page 5183). Is our interpretation correct?

This sounds correct to me.

...regards...dave case