Re: AMBER: atomic clash or structure size?

From: David A. Case <>
Date: Wed, 3 Sep 2003 08:32:42 -0700

On Tue, Sep 02, 2003, wrote:
> BOND = 216.5081 ANGLE = 905.7987 DIHED =
> 2173.1263
> VDWAALS = 67435606.3650 EEL = -4909.3228 HBOND =
> The vdwaals energy suggests some type of atomic clash, but the error
> message about the virtual box suggests that there is a problem in the
> size of the receptor. Which one is it?

Here's what happens: given the tremendously high vdW energy, the minimizer
thinks it has to move those atoms a long way to relieve the strain. Hence
it makes an enormously large first step, which exceeds the "virtual box" of
30 Ang. that surrounds the molecule.

The cause of the problem is the close overlap of atoms in the initial
structure; the symptom is that the box dimension requirements are violated.
You need to fix the cause, not the symptom.

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Sep 03 2003 - 16:53:01 PDT
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