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From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Mar 15 2010 - 15:05:46 CDT

This time, I've got a Desmond trajectory for a protein+ligand. When I align to frame 1 using the RMSD Trajectory Tool, the traj animation indicates alignment - the protein remains stationary in the window, whereas before it jumped around a great deal. However the ligand is still wrapping. Even worse, when I calculate the backbone RMSD, there are large jumps in it, indicating that the aligned traj is not what is being used to compute backbone RMSD [unlike the case of NAMD trajectories].

 

Can you shed light on this, or should I contact the Desmond developers?

 

Thanks!

Irene Newhouse
                                               
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