Hi Thanks for the reply.
Here is the link of the datasheet (http://www.atmel.com/Images/Atmel-2549-8-bit-AVR-Microcontroller-ATmega640-1280-1281-2560-2561_Summary.pdf) and the board I am using (http://store.3drobotics.com/products/apm-2-6-kit-1) or (http://copter.ardupilot.com/wiki/common-apm25-and-26-overview/)
In the decription its says pin 10, 11 or something but pin 10 in datasheet is VCC. I guess they are referring to PCINT10. I am not sure if you know which pins should work please let me know.