AMBER Archive (2006)

Subject: Re: AMBER: strange mm_pbsa output

From: alfredoq_at_fcq.unc.edu.ar
Date: Sun May 14 2006 - 09:22:14 CDT

Thanks Dr. Case for the help, that was the problem (nobox),
best wishes

Alfredo Quevedo

Quoting "David A. Case" <case_at_scripps.edu>:

> 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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