I just spent a couple of hours trying to figure out why I couldn't connect to my first ATSAM51D board. I was using a 2x5 0.05"-pitch cable that I've used for many different ARM debuggers/programmers. But it turns out that the one you need to connect to the Atmel ICE is NOT that cable -- it requires the ends to be reversed (i.e. connectors facing different ways on each end so that pin 1 goes to pin 10). Yuck!
So be sure to use the cable from the Atmel ICE box and not one from another ARM project. I'll be adding labels to both sides so I don't do this again in the future.
Anyways if anyone else runs into it here are some error terms I was searching for during the debugging:
Target Voltage reading too high
The good news is that the Atmel ICE seems to be pretty robust as it still works even though I had the pinout reversed for awhile.