Hopefully fixed by
https://github.com/Amber-MD/cpptraj/pull/1081
You will need to compile and use the GitHub version. As a bonus, you
should theoretically not need the 'namdcell' keyword for 'trajin' now,
as cpptraj should be able to distinguish between an actual symmetric
shape matrix and NAMD-style unit cell params in a DCD trajectory. Give
it a try and let me know if it works as expected.
-Dan
On Sat, May 18, 2024 at 2:36 PM Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> Thanks Dan for your very quick answers.
>
> Enjoy your weekend
> Vlad
>
>
> Get BlueMail for Android
> On 18 May 2024, at 20:25, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Hi,
>>
>> Thanks again for the report and for providing the files for
>> reproducing the bug. It looks like the issue is just in the input
>> trajectory setup routine, so hopefully it will be a quick fix. I'll
>> keep you updated.
>>
>> -Dan
>>
>> On Fri, May 17, 2024 at 10:54 AM Vlad Cojocaru via AMBER
>> <amber.ambermd.org> wrote:
>>>
>>>
>>> Dear Amber community,
>>>
>>> I have some simulations run with NAMD and I am trying to process them in
>>> CPPTRAJ using the following commands (just a simple example):
>>>
>>> parm file.top
>>> trajin file.dcd 1 last 2 namdcell
>>> center :1-172 origin
>>> autoimage anchor :1-172 familiar
>>> outtraj file.cdf netcdf
>>>
>>> When I do this CPPTRAJ from AmberTools 23 (using "ucell" instead of
>>> "namdcell"), everything runs fine. I just get these warnings but the
>>> netcdf trajectory is fine with correct periodic box information (I see
>>> the periodic images in VMD):
>>> Warning: CHARMM version is >= 22 but 'ucell' specified.
>>> Warning: Assuming box info is stored as unit cell and not shape matrix.
>>>
>>> However when I do exactly the same with CPPTRAJ in AmberTools 2024 (with
>>> "namdcell" instead of "ucell"), I get additional warnings and the netcdf
>>> trajectory does not contain the correct box information (periodic images
>>> do not show in VMD)
>>> Warning: CHARMM version is >= 22 but 'shape' not specified.
>>> Warning: Assuming box info is stored as unit cell and not shape matrix.
>>> Warning: Box Y vector length is zero.
>>> Warning: Box information present in topology but not in trajectory.
>>> Warning: DISABLING BOX in topology 'sox2_fgf4_hs_01_box.top'!
>>>
>>> Does anyone have any idea what is happenning here ?
>>>
>>> Thanks a lot
>>>
>>> Best wishes
>>> Vlad
>>>
>>>
>>> --
>>> Dr. Vlad Cojocaru (PD, Habil.)
>>> ________________________________
>>>
>>> Guest Scientist / Fmr. Project Group Leader
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> ________________________________
>>>
>>> Email:vlad.cojocaru.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
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Received on Sun May 19 2024 - 13:30:02 PDT
