I found the reason why the connection was not working, it was because the connection was trying to connect to port 8888, when it needed to connect to port 8889.
$conn = new PDO("mysql:host=$servername;port=8889;dbname=AppDatabase", $username, $password);
This fixed the problem, although changing the server name to localhost still gives the error.
Connection failed: SQLSTATE[HY000]  No such file or directory
But it connects successfully when the IP address is entered for the server name.