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 - 08:00:02 PDT
