In this tutorial, we will use Normal Mode Wizard (NMWiz), a VMD plugin that serves as a GUI for ProDy, to perform ANM analysis on the SARS-CoV-2 RBD. We will visualize the results in a cross-correlation map and square fluctuation plot and then produce ANM animations showing the predicted range of motion of the SARS-CoV-2 spike RBD.
Before starting, make sure that you have installed VMD and know how to load molecules into the program. If you need a refresher, visit the Multiseq tutorial.
First, load the SARS-CoV-2 spike protein/ACE2 enzyme complex (6vw1) into VMD. Then, start up NMWiz by clicking
Extensions > Analysis > Normal Mode Wizard.
A small window will open. Select
We want to focus on the RBD of SARS-CoV-2, so we need to choose a new selection. In
ProDy Interface, change
protein and chain F and click
Select. Next, make sure that
ANM calculation is selected for
ProDy job:. Check the box for
write and load cross-correlations heatmap. Finally, click
Note: Let the program run and do not click any of the VMD windows, as this may cause the program to crash or become unresponsive. The job can take between a few seconds and a few minutes. When the job is complete, you will see a new window
NMWiz - 6vw1_anm ... and the cross=correlation heatmap appear.
Now that the ANM calculations are completed, you will see the visualization displayed in
VMD Main. Disable the original visualization of
6vw1 by double-clicking on the letter
D. The letter will change red to indicate that it has been disabled.
OpenGL Display, you can see the protein with numerous arrows representing the calculated fluctuations.
To visualize the protein movements as described by the arrows, we need to create the animation. Return to the
NMWiz - 6vw1_anm... window and click
Make next to
VMD Main should now show a new row for the animation.
The animation should also be visible in
OpenGL Display. However, the previous visualizations are somewhat in the way. We can disable them in the same way as before by double-clicking the letter
You should now be able to see the animation of the ANM fluctuations of 6vw1, as shown in the figure below.
We now will return to the main text and interpret our results.