Hi,
Is the trajectory small enough that you could send it to me off list (along
with a topology or pdb) so I can reproduce the issue and come up with a fix?
-Dan
On Sat, May 18, 2024 at 3:04 AM Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Dan,
>
> Thanks for answering
>
> If I remove the namdcell keyword I get these for every frame. The netcdf
> is not readable.
>
> Warning: Set 2761; unit cell is not X-aligned. Box cannot be properly
> stored as Amber NetCDF trajectory.
> Warning: Set 2762; unit cell is not X-aligned. Box cannot be properly
> stored as Amber NetCDF trajectory.
> Warning: Set 2762; unit cell is not X-aligned. Box cannot be properly
> stored as Amber NetCDF trajectory.
>
> I guess the fact the cpptraj from AT23 with the "ucell" keyword processes
> these trajectories correctly means that the trajectories written by NAMD
> haven't changed. I also haven't seen any report on changes in the way NAMD
> writes the dcd files.
>
> Cheers
>
> Vlad
>
>
>
>
> On 5/17/24 17:04, Daniel Roe wrote:
>
> Hi,
>
> There were some recent issues regarding how unit cell information is
> stored in charmm (dcd) trajectories (see e.g.https://github.com/openmm/openmm/issues/4405 andhttps://github.com/Amber-MD/cpptraj/pull/1064). What happens if you
> omit the 'namdcell' keyword?
>
> -Dan
>
> On Fri, May 17, 2024 at 10:54 AM Vlad Cojocaru via AMBER<amber.ambermd.org> <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.dehttp://www.mpi-muenster.mpg.de/43241/cojocaru
> _______________________________________________
> AMBER mailing listAMBER@ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>
>
> --
> 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.dehttp://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 18 2024 - 04:00:02 PDT
