In mesh edit mode you can hide any vertices that you don't want to affect. Only visible vertices will be deformed.
Before calling the tool, select some vertices and use any of these default Blender shortcuts to hide what you want:
- H (Hide Selected)
- Shift + H (Hide Unselected)
- Alt + H (Unhide All)
This happens when you're editing a shapekey of your mesh that's set to a value of zero: the mesh won't seem to change, as that shapekey is not being displayed.
Set the value of the shapekey to 1.0 (in the shapekey settings) to see the mesh deforming with the tool.