AMBER Archive (2008)

Subject: Re: AMBER: help...ptraj does not output bounding box info

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Sep 03 2008 - 11:22:18 CDT

> No, the bounding box info is in "file.crd", one for each frame within
> "file.crd".

The prmtop has a flag to indicate whether there is a box. If it is
0, there is a chance that the box coords in the crd will be treated
as atom coordinates, making a hash of the output. If it is 1, there
is probably still a default set of box crds at the end of the prmtop.
If it is 2 the box is a truncated octahedron and likewise crds are
probably still at the end of prmtop even tho these may not be used.

Bill
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