make sure to type "&" after the command you want to run. This makes it run in the background. So you would need to type "AMBEServer &" in the terminal without the quotes to make it run after you close the terminal. Do not put the quotations. just type the command that is inside the quotations.
Type this into the Terminal:
This should run the application in the background.. You can check that it is running using:
ps aux | grep AMBEServer