You need to make sure that you can flash the arduino bootloader again onto the chip.

For this you need an programmer like the AVR Dragon.

This is the wiring connection for the AVR Dragon to the Trigorilla ISP connector:

To flash the bootloader, download and install avrdude:

• http://download.savannah.gnu.org/releases/avrdude/
• http://download.savannah.gnu.org/releases/avrdude/avrdude-6.3.tar.gz

• http://www.nongnu.org/avrdude/user-manual/avrdude_18.html#Unix

gunzip -c avrdude-6.3.tar.gz | tar xf -
cd avrdude-6.0
./configure
make
su root -c 'make install'

In /etc/udev/rules.d add (obviously as root user) the following file: 45-atmel.rules

# Atmel Corp. Dragon
ATTR{idVendor}=="03eb", ATTR{idProduct}=="2107", MODE="660", GROUP="dialout"

Then reload udev rules with:

sudo udevadm control --reload-rules && udevadm trigger

Steps and information below basically follow the description from here.

A bootloader can be found in the arduino directory from where you downloaded the arduino IDE itself. The location for Arduino-1.8.5 is:

Original bootloader:

arduino-1.8.5/hardware/arduino/avr/bootloaders/stk500v2/Mega2560-prod-firmware-2011-06-29.hex

or the newer one that fixes the WDT and the !!! problems¹⁾:

arduino-1.8.5/hardware/arduino/avr/bootloaders/stk500v2/stk500boot_v2_mega2560.hex

avrdude -p m2560 -P usb -c dragon_isp -v

avrdude -p m2560 -c dragon_isp -P usb -Ulock:w:0x3F:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m -e -v

avrdude -p m2560 -c dragon_isp -P usb -Uflash:w:stk500boot_v2_mega2560.hex:i -Ulock:w:0x0f:m -v

• https://learn.sparkfun.com/tutorials/installing-an-arduino-bootloader/all