After installing avrdude, create a file avrdude.rc in the same directory as your avrdude.exe (Windows) or a file .avrduderc in your home directory (Linux) with the following content:

default_serial = "com10";
default_programmer = "stk500v2";

(change your settings as needed). After this is set up, you can use avrdude without entering these settings each time. This also makes it possible to leave this parameters out of the makefiles.

Connect the ATMega to power and the ISP connector.

Try to read out the fuses:

avrdude -p ATMEGA328P -U lfuse:r:-:h

(use ATMEGA328P or ATMEGA168 for the microcontroller model and use the appropriate ISP com port).

You should get something like:

0x62
avrdude: safemode: Fuses OK

If not, check all connections or if you have a shortcut.

You can use “lfuse” for low fuses, “hfuse” for high fuses and “efuse” for extended fuses.