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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 18 2024 - 11:30:02 PDT
