Re: AMBER: Bug: ptraj adds spurious box information

From: David A. Case <>
Date: Fri, 13 Aug 2004 15:13:33 -0700

On Fri, Aug 13, 2004, Don Bashford wrote:

> According to Appendix E of the Amber 8 Manual, box information should be
> written to traj files only for periodic systems, and indeed, this is how
> sander behaves. But ptraj, given a parm file for a non periodic system
> (i.e. one in which IFBOX=0), produces an output traj file with spurious
> periodic box info given as three zeros.

You have to use the "nobox" option in your trajout line to suppress the
spurious box output. It could perhaps be viewed as a bug that ptraj doesn't
do this automagically; I say "perhaps" only because I didn't write the code,
and there may be some underlying reason why this is not done.

....good luck...dac
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Received on Mon Aug 16 2004 - 09:53:01 PDT
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