Hi Dan,
Actually adding the "ucell" keyword to the "trajin" command in the
github version of cpptraj solves the issue (but only in the github
version) .... Is this update planned to be included in Amber16 soon ?
Best
Vlad
On 01/31/2017 01:16 PM, Vlad Cojocaru wrote:
> 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 - 05:00:02 PST
