On Tue, Jan 31, 2017 at 7:32 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> Actually adding the "ucell" keyword to the "trajin" command in the
> github version of cpptraj solves the issue (but only in the github
> version) ....
Glad to hear the GitHub version works for you.
> Is this update planned to be included in Amber16 soon ?
The convention for cpptraj GitHub -> AmberTools has been to only port
over bug fixes to cpptraj and leave new functionality for AmberTools
releases (next one should be around April or so I think). Technically
this is a case of NAMD not following the CHARMM format and not a bug
in cpptraj :-), but if I get a chance I'll try to make a fix (sadly I
don't have as much time as I'd like for cpptraj development anymore).
Until then hopefully the GitHub version of cpptraj will work for you.
Thanks for the report,
-Dan
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 31 2017 - 05:30:03 PST
