Thanks a lot Dan
Best
Vlad
On January 31, 2017 6:48:08 PM GMT+01:00, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>On Tue, Jan 31, 2017 at 9:16 AM, Vlad Cojocaru
><vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>
>> 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.
>
>The CHARMM format has actually stored the shape matrix instead of unit
>cell parameters since version 22. When I wrote the cpptraj Charmm DCD
>trajectory parser I erroneously omitted the conversion to and from the
>shape matrix (note that I think ptraj may have handled this correctly
>so this is my mistake). I'm not sure what the history of Charmm DCD
>files is with NAMD, so I'm not sure if it was a conscious decision on
>their part to just store unit cell parameters. If it was then they
>should decrement the Charmm version number in the trajectory to at
>least 21 to reflect this (which is what cpptraj now does when writing
>unit cell parameters to Charmm trajectory files).
>
>>
>> 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.
>
>There are two related pull requests:
>https://github.com/Amber-MD/cpptraj/pull/399
>https://github.com/Amber-MD/cpptraj/pull/427
>
>Looks like the former was incorporated as update 16 while the latter
>hasn't yet made it to AmberTools.
>
>-Dan
>
>
>>
>> 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
>>
>>
>> _______________________________________________
>> 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
>
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--
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Received on Tue Jan 31 2017 - 10:30:03 PST
