The Atmel ICE Basic comes with a 50 mil 10 conductor cable that terminates in a 2 x 3 100 mill socket -and no documentation. With a good bit of digging around I found it attaches to the 6 pin header between the ATmega2560 and the reset button with the indexing tab facing the AT chip. Things were looking good and I loaded up a simple blinky program. With this cable it doesn't perform debug functions - the whole purpose of buying this thing - and when I went back to the Arduino software I now get a communication timeout and so far have not found a fix.
More digging suggested a custom hookup with a 10 pin 'squib' cable - a cable with 10 individual 100 mil connectors. These are the connections you need
Signal AVR Arduino Function
pin mega pin
TCK 1 A4 Test Clock
TMS 5 A5 Test Mode Select
TDI 9 A7 Test Data In
TDO 3 A6 Test Data Out
nTRST 8 ? Test Reset (optional, only on some AVR devices).
nSRST 6 Reset* Reset (optional) Used to reset the target device. Connecting this pin is
recommended since it allows the Atmel-ICE to hold the target device
in a reset state, which can be essential to debugging in certain scenarios.
VTG 4 VCC Target voltage reference.
GND 2, 10 Several Ground.
*Reset on the Power connector - it's the only reset on the schematic
These don't appear to be used in the JTAG connection:
MISO (6 pin header and pin 50)
MOSI (6 pin header and pin 51)
SIC (6 pin header and pin 52)
VCC and GND are used on the 6 pin headers as a reference, It is also available on IOREF and 5V on the Power header, and the 5V and GND pins on the digital header.
Has anyone hooked up an Atmel ICE with this arrangement? The cable is ridiculously expensive - about $50 for maybe $5 of components. If someone has tried it and it fails I'd rather not spend the money.