AMBER Archive (2006)

Subject: Re: AMBER: strange mm_pbsa output

From: David A. Case (case_at_scripps.edu)
Date: Sat May 13 2006 - 17:44:14 CDT

On Sat, May 13, 2006, alfredoq_at_fcq.unc.edu.ar wrote:

> Thanks Ray for the hint. The complete mdcrd file and the file with the
> stripped waters were very strange. After loading them in VMD the covalente
> structure was all messed up

The most common problem is that you did not specify "nobox" when you created
the stripped trajectory file with ptraj.

Of course, I'm just guessing here, but it's worth checking.

...dac

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