Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology)

From: Daniel Roe <>
Date: Tue, 31 Jan 2017 11:54:53 +0000


Debugging this is going to be tricky without access to the trajectory or
one like it. I assume this trajectory was not generated with charmm (if it
was let me know). It sounds like the trajectory may not correspond exactly
to the charmm format (which to be fair is not exactly well documented).
Contact me off list if there is some way I can get access to this or maybe
send me a smaller trajectory/topology that exhibits the same behavior.


On Tue, Jan 31, 2017 at 4:10 AM Vlad Cojocaru <> wrote:

> Dear all,
> I am having an issue with cpptraj when trying to image DCD trajectories
> back into a truncated octahedron box. I am uising Amber 16 on a
> supercomputer and as its a brand new compilation, all updates are
> installed. I have an amber topology (parm7) and a number of DCD
> trajectories. "autoimage familiar" actually gives me a strange cube
> instead of the normal truncated octahedron.
> Now when I run the same job on my workstation with a version of Amber 16
> compiled in July 2016, I actually get the correct truncated octahedron.
> Therefore, I suspect this might have something to do with some very
> recent updates of cpptraj and the way the program reads the information
> from DCD files.
> In the cpptraj output I found these lines which may be relevant
> Warning: oct4_sox2_hoxb1_mur_01_box_cmd0101.dcd: Reported number of
> frames in DCD file is 0,
> Warning: actual number of frames is 6000. Only reading 6000 frames.
> Version >= 22; assuming shape matrix is stored.
> Warning: Trajectory box type is 'Non-orthogonal' but topology box type
> is 'Trunc. Oct.'.
> Warning: Setting topology box information from trajectory.
> I also found an earlier related thread in which Dan Roe suggested to use
> the "ucell" keyword for the "trajin" command as a fix but this does not
> fix the issue.
> I'd appreciate knowing if there is a way to fix this behavior or if I
> need to revert some of the updates.
> Thanks a lot for answering
> Best wishes
> Vlad
> --
> Vlad Cojocaru, Ph.D., Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]
> _______________________________________________
> AMBER mailing list
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Jan 31 2017 - 04:00:02 PST
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