[Chimera-users] Load AMBER parm/traj from command line.

Elaine Meng meng at cgl.ucsf.edu
Tue May 19 10:24:34 PDT 2015


Hi Rodrigo,
Yes, you can specify input to MD Movie (trajectory viewer) in the Chimera startup command by using a metafile.  A metafile is simply a text file with the same information as you would have typed into the MD Movie input dialog.  The different trajectory formats have different numbers of things you need to input, as you can see from looking at the MD Movie input dialog, but here’s one example of a metafile for an AMBER trajectory:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile>

First you would need to figure out how to start Chimera from the system command line (depends on the system):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html>

Then you would specify the metafile input in that command line with prefix “md:” or “movie:”.  For example, if just typing "chimera" starts chimera on your system and you had named your metafile “myfile.txt” it would be something like:

system prompt> chimera md:myfile.txt

Prefixes for different input file types:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 19, 2015, at 10:10 AM, ros <rodrigogalindo at gmail.com> wrote:
> 
> Hello!
> Is it possible to start up chimera and have it load an AMBER topology and trajectory file?
> For example, in Linux, you can start VMD with:
> 
> vmd -parm7 name.prmtop -netcdf traj.nc
> 
> And will load the topology with the corresponding trajectory frames.
> In chimera we do that using the 'Get Ensemble info' window in the MD movie tools.  Is it possible to do it in a single line?
> Thank you!
> Rodrigo.




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