AMBER Archive (2008)

Subject: Re: AMBER: Minimization in Octahedric Box

From: David A. Case (
Date: Tue May 06 2008 - 12:28:20 CDT

On Tue, May 06, 2008, wrote:
> Unfortunately at the end of the minimization run, I realized that the box
> was deformed and in particular 6 satellite clouds of water appeared around
> the main cloud surrounding the peptide (see attached files).

This sounds like an imaging issue. Did you use ptraj to put re-image the
coordinates into the primary box, before doing the visualization?
Be sure to use the "familiar" option to get things to look like an octahedron.
See the "image" command in the ptraj section of the manual for details.


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