Re: [AMBER] ptraj: box information for truncated octahedron

From: Ignacio J. General <>
Date: Thu, 24 Mar 2011 13:24:08 -0400

Thomas, when I use ptraj to extract frames from a trajectory, using the
restart format, I don't have the problem you do. My frames have the correct
box info at the end of the rst files.

Do you have the right box information in the parameter file (look under
%FLAG BOX_DIMENSIONS)? I know that the info in the restart file is the
important one, but maybe in ptraj, for some reason, the info in the
parameter file is also important?

I hope this helps,


On Thu, Mar 24, 2011 at 1:10 PM, <>wrote:

> Hi,
> 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?
> Thanks,
> Th.
> 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
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Received on Thu Mar 24 2011 - 10:30:05 PDT
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