From: andrew ritchie (
Date: Wed May 18 2011 - 13:30:54 CDT


I am trying to align multiple trajectory files (.xtc) to a single .pdb file
from a python script (which will also catalog the coordinates of a specific
R chain relative to that .pdb file, among other things). The best I can
figure would be to write a tk script and execute it from python using
os.system("vmd -e tkscript"). I do not know how I would construct this tk
script though. I can't even seem to load a trajectory file (with the
accompanying .gro file) with another structure file, as vmd -m considers
each line an independent file, rather then vmd <trajectory> <structure>
being a single file.

Andrew Ritchie
The University of Texas at Austin
Chemistry Graduate Student