From owner-chemistry@ccl.net Sun Jul 22 19:18:01 2007
From: "David A. Case case[#]scripps.edu" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: AMBER PBC box alignment
Message-Id: <-34778-070721222853-14611-HygKmlyGBw6FoQNriwRIQQ,,server.ccl.net>
X-Original-From: "David A. Case" <case++scripps.edu>
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Date: Sat, 21 Jul 2007 18:56:48 -0700
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Sent to CCL by: "David A. Case" [case:_:scripps.edu]

On Sat, Jul 21, 2007, Jun Cui juc9+]*[pitt.edu wrote:
> 
> 
> Does amber 9 need the periodic box to be parallel to the xy, yz, and xz 
> planes? 

Amber supports general triclinic unit cells, but the "a" axis must be along
the x direction, and the plane containing "a" and "b" must be in the xy plane.
(If the unit cell is a rectangular parallelopiped, this implies that box edges
are parallel to xy, yz and xz.)  I don't know of a simple code that will do
the conversion, however.

....dave case