Why the programming USB port can not upload program into the ATSAM3X8E?

Hi, I followed the schematic of Arduino Due and made an DIY mainboard based on the ATSAM3X8E and ATMEGA16U2.

Currently, the Native USB port of my mainboard works well. But the Programming USB port does not work. I can write the firmware to the ATMEGA16U2 by using an Arduino UNO as ISP programmer. The Arduino development software also can detect and recognize this programming USB port. However, when I upload the program using this port, the Arduino development software says "NO Device on COM xx".

I really can not understand why this happen? The schematic of my design is the same as Arduino Due.

Could anyone give me some suggestions?

Hello ybs273,

I have the same problem with my "copy-version" of the Arduino Due and don't get in working. The Tx of the ATMega16U2 is connected to an Levelshifter (SN74LVC1G125DCKR) and then connected to the Rx of the ATSAM3X8E. The Rx of the ATMega16U2 is directly connected to the Tx of the ATSAM3X8E. I put the Arduino Firmware on the ATMega16U2 so Windows recognizes the Chip as Arduino Due. If I now want to programm the "Due" it ends with this lines:

C:\Users\Max\AppData\Local\Arduino15\packages\arduino\tools\bossac\1.6.1-arduino/bossac.exe -i -d --port=COM6 -U false -e -w -v -b C:\Users\Max\AppData\Local\Temp\builda4befd116142090320683143dfa787f4.tmp/test_v72_DUE_Icons.ino.bin -R
Send auto-baud
No device found on COM6
Set binary mode
Beim Hochladen des Sketches ist ein Fehler aufgetreten (German for an error occurred...)

Do you found an mistake at your build or does anyone else know what could have been wrong?

Greets, Max