Re: AMBER: Minimized structure

From: Thomas E. Cheatham, III <>
Date: Thu, 28 Jul 2005 21:09:55 -0600 (Mountain Daylight Time)

> Regards. I'm glad and thankful for your kind
> explanation and I'm taking your advise to do a
> "checkoverlap" to check for oo close contacts.
> However, I'm facing some technical problem now as I do
> not know how should I understand the output file.

The output from checkoverlap comes right to the screen (stdout/stderr);
you do not need to trajout an output trajectory (but you do need to read
input coordinates with trajin). If there are any overlaps, ptraj will
tell you (with output text starting with "OVERLAP"). If there are none,
then nothing will be reported.

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Received on Fri Jul 29 2005 - 04:53:00 PDT
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