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@cgl.ucsf.edu http://www.cgl.ucsf.edu