VMD-L Mailing List

From: Chris Ing (ing.chris_at_gmail.com)
Date: Wed Dec 19 2012 - 11:36:22 CST

I'm trying to make a more responsive game out of an Interactive MD
simulation.

The game might simply be a protein and ligand in a box and the objective of
the game is to dock the ligand such that it satisfies some positional or
energetic criteria. I believe that numerous people, including me, have done
this simulation using interactive MD.

The catch is that I'd really like to find a way to tell the gamer that they
have succeeded. Ideally, the VMD representation (color) of the complex
would gradually change the closer they got to the correct solution,
however, I'm not sure that's possible.

I've briefly looked at the "imdmenu1.0" plugin and in particular the
callback whenever a new frame is received. This seems like a good starting
point. From here I could initiate a naive distance check between the known
final position of the ligand in the binding site and the position of the
ligand at the current frame. Then I could update the VMD representation
accordingly.

Is this the best approach for real-time processing of the interactive MD
data? Is there an similar TCL script (perhaps an existing plugin) that
computes distances between regions of a protein that I could borrow from?

Thanks for your time,
-Chris Ing
University of Toronto