Periodicity Question

From: DeLano, Warren <>
Date: Fri 20 Sep 2002 17:29:49 -0700

A quick question for some Amber guru...

If one is using a truncated octahedral periodic box, it orthogonality assumed even if BETA is not equal to 90.0 in the prmtop? or is the truncated octahedron instead built using the lattice of the parallelopided with the indicated BETA?

Why am I asking? Because in testing the PyMOL trajectory reader, I've been given a couple of prmtop files which have BETA of 109.47 and IFBOX=2 (truncated octahedral). The resulting images look okay by eye if imaged against an orthorhomibic truncated octahedron (assuming BETA=90), but rather tweaked if I used the BETA provided.

Is my code broken, or is BETA assumed to be 90.0 with a truncated octahedron?


Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501
Received on Fri Sep 20 2002 - 17:29:49 PDT
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