On Mon, Feb 29, 2016 at 8:31 AM, Song-Ho Chong <chong.sookmyung.ac.kr> wrote:
> 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.
What does the first line of your trajectory file look like?
> 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 },
Be aware that modifying the code in this way may prevent updates from
successfully applying.
> Then, cpptraj works fine.
> (There was another problem ... I had to manually add
> parmbox alpha 90 beta 90 gamma 90
> to use autoimage.)
Your topology/trajectory combination must be very strange to encounter
these issues. One of the many disadvantages of working with ASCII
trajectories instead of NetCDF is that since box angles are typically
not stored in Amber ASCII trajectories, cpptraj is reliant on the box
information in the Amber topology file. Does your topology not contain
a '%FLAG BOX_DIMENSIONS' section?
-Dan
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Feb 29 2016 - 08:00:06 PST
