[Chimera-users] Load AMBER parm/traj from command line.
rodrigogalindo at gmail.com
Tue May 19 10:26:48 PDT 2015
This is perfect!
Have a good day,
On Tue, May 19, 2015 at 11:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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:
> First you would need to figure out how to start Chimera from the system
> command line (depends on the system):
> 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:
> I hope this helps,
> 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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