Hi, maybe I'm missing the mark here, but:
You can't debug because the AVR is a different processor than your pentium-ish one, so your gdb debugger can not step through the instructions. You need either an AVR simulator or a hardware connection to your AVR so the debugging takes place in-hardware.
If you are using Windors you can use AVRStudio to debug (free). For a hardware debug, you should use JTAG or debugWire depending on the AVR you are using. AVRStudio is very easy and simulates every register, peripheral and IO port on the AVR.
Hope it helped!
Regards,
Alex