The srv.pde "software" is actually a server script which you need to upload and run on the Arduino. It is this script which enables Matlab to communicate with and control the Arduino.
The srv.pde sketch is supplied in the Matlab Arduino support package here:
You upload it to the board just like you would any other standard sketch. Full instructions are contained in the readme file that comes with the support package... quoted snippet here:
"UPLOAD SRV.PDE (OR ADIOSRV.PDE) TO THE ARDUINO BOARD (to be done only once):
The srv.pde (or adiosrv.pde) is the "server" program that will continuously run on the microcontroller. It listens for MATLAB commands arriving from the serial port, executes the commands, and, if needed, returns a result.
The following instructions are needed to upload the srv.pde file into the controller's flash memory. Note that if you don't have the motor shield and don't plan to use it, then you can UPLOAD THE ADIOSRV.PDE file instead the instructions are the same, except for the folder location).
As long as no other file is uploaded later, this step does not need to be repeated anymore, and the package can be used as soon as the board is connected to the computer..... "
Follow the instructions in the readme, these will walk you through uploading srv.pde to your Arduino and should solve your problem.