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Has anyone tried to program the Arduino Mega with an FTDI chip like in the Arduino Nano (this is for a custom design)

Will it work?

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That will work. The only think to look out for is how to reset the board. Either manually reset it before uploading, or connect the DTR pin of the FTDI, via a capacitor, to the reset pin. – Gerben Mar 12 '15 at 16:46
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It actually worked! – Arcu Apr 7 '15 at 20:34
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The Arduino Mega already has a built-in USB-UART bridge, so there's no need for a separate chip.

The ATmega1280 on the other hand is just a bare AVR MCU and does require either a separate USB-UART bridge for serial programming (provided it is programmed with an appropriate bootloader) or an ISP programmer for ISP programming.

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Sorry, I expressed my self wrong. My goal is to program the Atmega2560 (with the bootloader already burned in) with the FTDI chip instead the AVR USB bridge from the Arduino Mega original design. Do you think that might work assuming the connections are correct? Or in other words, is the Arduino IDE expecting some sort of response from the programmer that the AVR bridge will provide and the FTDI will not? – Arcu Mar 12 '15 at 15:01
    
The FTDI chip is a USB-UART bridge, so I would expect not. But to be perfectly honest, I'd use a ISP programmer and save myself the cost of the bridge and the time of burning the bootloader. – Ignacio Vazquez-Abrams Mar 12 '15 at 15:29
    
Your comment seems either confusing or wrong. Why would you expect an FTDI bridge not to work, when it is what the official Arduino Mega actually utilizes? The Arduino IDE doesn't speak USB for the ATmega boards anyway; it relies on the host operating system to present a Serial API, so it has no idea of the implementation detail to tie to a particular board. – Chris Stratton May 11 '15 at 19:41
    
@ChrisStratton: "... is the Arduino IDE expecting some sort of response from the programmer that the AVR bridge will provide and the FTDI will not?" – Ignacio Vazquez-Abrams May 11 '15 at 19:45
    
If you think there is a difference there you are quite mistaken. The bridge is merely a proxy. The response comes form the bootloader on the target MCU. As I'd mentioned previously the IDE (avrdude actually) relies on the operating system Serial API. It doesn't care what USB bus operations or VID/PID are involved. It merely cares that whatever operating system Serial device you point it at in the menu has a bootloader that responds at the baud rate configured for the board entry. Take a look in boards.txt at the FTDI- vs. ATmega16u2 interfaced boards. – Chris Stratton May 11 '15 at 19:48
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In fact, the basic Arduino Mega (with the ATmega 1280) utilizes an FT232RL, so yes, it will work if you connect it correctly.

It is only the newer Mega2560 (along with the similar-generation Uno, etc) which utilizes an ATmega16u2 or similar as the USB bridge.

Generally speaking, the bootloader doesn't care - you should be able to use either target chip with either USB bridge (or others).

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