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

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Tue, 31 Jan 2017 10:10:02 +0100

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 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]mpi-muenster.mpg.de
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Received on Tue Jan 31 2017 - 01:30:03 PST
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