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 and
https://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> 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
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Received on Fri May 17 2024 - 08:30:02 PDT
