Hi Dan,
Thanks for your feed-back ...
The trajectories were calculated with NAMD 2.11 and 2.12 ... I thought
of doing one last check using the github version of cpptraj with the
"ucell" keyword ... If this also does not solve the issue, I will
provide you the top and trajectory file off the list
Best
Vlad
On 01/31/2017 12:54 PM, Daniel Roe wrote:
> Hi,
>
> 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.
> Thanks,
>
> -Dan
>
> On Tue, Jan 31, 2017 at 4:10 AM Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> 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]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
--
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
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Jan 31 2017 - 04:30:02 PST
