In order to change the owner of the Controller, complete the following steps.
chown -R <New User>:<User Group> <Controller Folder>
Oops you've accidently started your controller with root user instead of your app service user (ie appd, appdynamics, etc...) ?
1. First stop controller (as root)
2. As root, change permissions back to original user and group
chown -R <original user>:<original group> <controller home>
Ie: chown -R appd:appd /opt/appdynamics/controller
3. Start controller with your original user.
Good tip @Eli.Rodriguez Thanks for contributing.