AMBER Archive (2003)

Subject: Re: AMBER: sander minimization

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 29 2003 - 16:32:55 CDT

On Fri, Aug 29, 2003, atobak_at_eden.rutgers.edu wrote:

> After running sander for minimization, my job exited immediately and the
> results I got were as follows:
>
> VDWAALS = ************* EEL = -4905.2935 HBOND =

You probably have two atoms almost on top of each other in your starting
structure. Using the "checkoverlap" command in ptraj is one way to find
out which atoms are involved.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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