[Chimera-users] movies of gromos files

[Eric Pettersen]

On Mar 1, 2006, at 12:41 PM, John Robinson wrote:

> Trying to visualize gromos trajectories.  The Tk popup is asking for
> three files: Topology, Coordinates, and PROMD.  I don't seem to be
> giving it the files it needs.  What are the file extensions
> corresponding to these file types? (.top, .trr, .tpr)?

Topology is your topology file, almost undoubtedly the one ending  
in .top.  It has sections such as TOPPHYSCON, TOPVERSION, and  
ATOMTYPENAME in it.

Coordinates is the output trajectory coordinates.  Most likely  
your .trr file.  Chimera can only read formatted, not binary, GROMOS  
trajectories.  It contains sections such as TIMESTEP and POSITIONRED.

PROMD is one of the input files used to create the trajectory (the  
output files don't contain all the info necessary to properly display  
the trajectory).  It has sections such as SYSTEM, BOUNDARY, and WRITE.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu