Running a scheduled Linux Command?

I’m using AMP as a personal application manager, and do not need to worry about access control. With that in mind, is it possible to schedule a Linux command to be run via the Mincraft panel? In this case, my server is not being cleanly shut down (something is hanging somewhere…) and AMP doesn’t kill the java process. In order to combat this, I’d like to run a shell script to find and kill the java process that’s being run. I have the script in-hand, but cant figure out how to schedule it to be run.

Is there any way to do this? Or suggestions for another approach?

Is this a modded server? If so its probably one of the mods. Also giving users permission to run commands is a security risk, so probably not anytime in the future. It would be best to find out the reason its failing to stop instead.