Dear all,
I've just updated the Amber24 and tried to image a trajectory with AMBER
topology (generated in Leap with a truncated octahedron) and DCD files
generated by NAMD3 (commands below). First I did not use the "namdcell"
keyword and this gave me a netcdf trajectory with a cubic box although
my box is a truncated octahedron in the topology and triclinic in the
DCD files. When I included the "namdcell" keyword, the cpptraj output
told me very weirdly that my trajectory does not have box information
and the box info from the topology will be disabled. The trajectory was
not imaged in this case.
When I did the same (with the "namdcell" keyword) with a CPPTRAJ version
from May 24 2024 from Github (following a similar issue I posted on the
CPPTRAJ
Github) the imaging worked correctly.
Of course, I can still use that version of CPPTRAJ (or the newest from
Github) but I think it is
dangerous to have this bug not fixed in the AMBER code since people may
be using imaging as an intermediate step without saving the trajectory
with the entire box. If people process the raw trajectories and save
just a layer of waters around the protein (like we do normally) the
resulting trajectories will be wrong.
Best wishes
Vlad
parm ${datadir}/${model}_box.top [p0]
trajin ${datadir}/${model}_box_${sim}01.dcd 1 last 100 namdcell parm [p0]
center $molmask origin
autoimage anchor $molmask familiar
outtraj ${model}_box_${sim}_${t}.cdf netcdf parm [p0]
run
--
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 Mon Mar 31 2025 - 03:30:02 PDT
