RMSD fitting and analysis of a trajectory

Trajectory frames are going to be superimposed to a reference frame in such a way that the root mean squared distance (RMSD)

\[\mathrm{RMSD} = \sqrt{\frac{1}{N} \sum_{i=1}^N (x_{a,i} - x_{b,i})^2}\]

is minimized.

Superposition

In order to more clearly show conformational changes, superimpose all trajectory frames on the CORE domain using Extensions ‣ Analysis ‣ RMSD Trajectory Tool

  1. selection widget (starts with protein): enter the selection for the CORE domain: protein and not (resid 30 to 59 122 to 159)
  2. Selection Modifiers: Backbone
  3. Reference Mol: Top
  4. RMSD: calculate RMSD (avg should be about 2.6 Å)
  5. ALIGN: superimpose all frames to the first frame
  6. RMSD: calculate RMSD (avg should be about 1.5 Å)
  7. File ‣ Plot Data to show CORE backbone RMSD over time
  8. visualize the trajectory

RMSD analysis

Task: Produce a timeseries of the backbone RMSD of the whole protein as a function of time (using Extensions ‣ Analysis ‣ RMSD Trajectory Tool)

Questions:

  • What is the maximum RMSD?
  • How does the RMSD change when you include
    • all atoms?
    • all heavy atoms (i.e., do not use hydrogens)?
  • Does your RMSD result depend on the previous superposition step?
  • Is the result consistent with the previous result of your RMSD analysis of the static structures?