Re: AMBER: reporting atoms clashed during simple energy minimization

From: David A. Case <>
Date: Tue, 9 Sep 2003 08:36:29 -0700

On Tue, Sep 09, 2003, wrote:
> I use sander for simple energy minimization (without molecular dynamic
> simulation). Is there any method that can report the atoms clashed during
> the minimization? For example, if the distance of the non-bonded atoms is
> less than 1.5 A, it can report the warning.

You can use the "checkoverlap" command in ptraj before or after the
minimization to look for clashes. If you need to check every step during the
minimization, you will have to add some print statements inside the code.

...good luck....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 Tue Sep 09 2003 - 16:53:01 PDT
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