spcomputing:
There are a couple of "flavors" for the Atmega328. The one that comes with the Uno R3 is the Atmega328P-PU which means this chip passed the low current operational testing at Atmel (Pico Power). If it does not pass this test it does not receive it's "P" badge and is just a Atmega328-PU. The problem is, it also receives a different chip ID and that causes the programmers to not program the chip. If you put an entry into the boards.txt file for the Atmega328-PU then it should bootload.
Thanks for your reply!
I've tried to google how to edit my boards.txt, but it didn't work. I even tried to edit my avrdude.conf also without any success.
I tried these steps: http://www.instructables.com/id/How-to-use-Arduino-Mega-2560-as-Arduino-isp/
and these: http://www.3guys1laser.com/blog-burn-bootloader-blank-atmega328atmega328p-arduino-uno
But still I can't manage to bootload my empty atmega328-PU without any error.
My setup:
I have an empty atmega328-PU on a breadboard with some wires coming from my arduino mega 2560.
I have a 100 nano capacitor between +5v and the reset on my mega(which I only use after uploading).
I have also tried to use a 16mhz crystal with 2x 20pico(both wired on ground).
And I have tried to put a 10k resistor between the reset and +5v
I think I've missed something crucial but I just can't find the problem.