Dear all,
I'm using pmemd.cuda to do simulations with a charmm force field.
Necessary inputs (Amber topology and initial coordinate files) were
generated with chamber.
With premed.cuda, Amber restart (.rst) and trajectory (.crd) files were
produced during the simulations.
I encountered the following problem when doing analysis with cpptraj.
First of all, no problem happens in cpptraj with restart files.
For example,
trajin my_file.rst
autoimage
trajout my_file.pdb pdb
correctly identifies the input restart file as "Amber Restart" and
Trajectory box type was set to Orthogonal based on the restart file.
However, a problem happens with Amber trajectory file.
For example,
trajin my_file.crd
autoimage
trajout my_file.pdb pdb
identifies the input crd file as "Charmm COR", generates
the error message, Error: No atoms in CHARMM COR file,
and cpptraj stops the execution.
To get around this problem, I replaced the following line
in TrajectoryFile.cpp
{ "Charmm COR", 0, 0, Traj_CharmmCor::Alloc },
with
{ "Charmm COR", 0, 0, Traj_AmberCoord:Alloc },
and recompiled cpptraj, so that my trajectory file recognized
as Charmm COR file be treated as if it is Amber trajectory file.
Then, cpptraj works fine.
(There was another problem ... I had to manually add
parmbox alpha 90 beta 90 gamma 90
to use autoimage.)
I just wonder whether there is a better way ... and
I would appreciate it very much if cpptraj could recognize
the file type just with file extension.
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Received on Mon Feb 29 2016 - 08:00:03 PST
