In UAV Toolbox Support Package for PX4® Autopilots, serial communication is supported over the native-USB port and non-usb ports (for example, /dev/ttyS6) on the Pixhawk Series boards. To achieve serial communication over non-USB serial port, a serial-to-USB FTDI converter is required.
The below image shows the connection between Serial 4 (/dev/ttyS6) on Pixhawk 1 board and the USB port on host computer, by using an FTDI converter.

The below table lists the serial pins on the Pixhawk 1 board and their FTDI mapping. The pins listed here are from left to right.
Pin and FTDI Mapping for Pixhawk 1
| Serial port on Pixhawk 1 | FTDI | |
|---|---|---|
| 1 | +5V | Not connected |
| 2 | Serial 4 Tx | FTDI Rx |
| 3 | Serial 4 Rx | FTDI Tx |
| 4 | Serial 5 Tx | Not connected |
| 5 | Serial 5 Rx | Not connected |
| 6 | GND | FTDI GND |
Once the above hardware connections are completed, open the Configuration Parameters
dialog box in Simulink, and set the serial port to dev/ttyS6 (go to
Hardware Implementation pane > Target Hardware
Resources > External Mode, and enter
dev/ttyS6 in the Hardware board serial Port
field). Now you can run the model in External mode over FTDI with Pixhawk 1
board.