Thanks Dan,
Sure, I understand the lack of time .... It works for me now locally and
I hope I will get it to work on the supercomputer I am using as well
(unfortunately I cannot do the analysis on my own machine because of
file transfer limitations).
If I understand correctly, this means that CHARMM changed the DCD
formatting which caused a recent update of CPPTRAJ to read those. But
this update made CPPTRAJ unable to correctly process NAMD DCDs because
NAMD did not update to the new CHARMM formatting.
Am I right here ? If yes, do you know which is precisely the update that
has changed CPPTRAJ behavior towards DCDs ? As I mentioned before, a
CPPTRAJ version compiled in July 2016 reads and processes NAMD DCDs
absolutely fine.
Best wishes
Vlad
On 01/31/2017 02:07 PM, Daniel Roe wrote:
> 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
>
>
--
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 - 06:30:03 PST
