Can a raspberry sink 5V
No, this is outside of the pi's electrical specs.
Use an NPN transistor (with base resistor) or better and more simply N-FET, either configured as an inverting &quot;low side switch&quot; to pull down the ATmega's reset line, in response to a positive output from the PI GPIO.
Also make sure you're performing appropriate level conversion on any UART or other signals between the pi and ATmega.