[AMBER] ptraj: box information for truncated octahedron

From: <thomas.fox.boehringer-ingelheim.com>
Date: Thu, 24 Mar 2011 18:10:35 +0100


I have a system with a truncated octahedron as my solvent box. Accordingly,
the last line of my restart file reads something like
27.141 27.141, 27.141 109.471... 109.471... 109.471

Now I noticed that when I use ptraj (Ambertools 1.4), the information that it
is a octahedral box seems to get lost when I use the commands
trajin input.crd
trajout output.crd restart

Then my last line in the generated restart file only has the x, y, z
dimensions of the box, but not the angles.

1) is this a problem? I would guess yes, as - if I understood the
documentation correctly - the box dimensions are taken exclusively from the
restart file.
2) I guess I could use the box command in ptraj to fix this - but I'd
rather have the box information (size *plus* shape) carried over to the
output file automatically. Is there an easy way to do this?


Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox

Boehringer Ingelheim Pharma GmbH & Co. KG
Lead Identification and Optimization Sup
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585

Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR B 23260

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Received on Thu Mar 24 2011 - 10:30:03 PDT
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