AMBER Archive (2007)

Subject: Re: AMBER: program bug?

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 12 2007 - 10:22:35 CDT

On Thu, Jul 12, 2007, M. Maeda wrote:
>
>
> I check the resulted trajectory files by using VMD. Some very long bonds
> assigned to protein (the color is gray and blue) could be seen between the
> outside and the inside of the protein.

Are you sure that "test.pdb" is a good structure? Were any of these
long bonds present before you started? If not, try to figure out exactly
which bonds are causing the problem. Run a short simulation (say 100 steps),
set ntpr to 1 to get lots of print-out, and study the results carefully.

...good luck...dac

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