You can download here the source code of the AutoDock + jMetal integration.
Download this file and uncompress it to install it. Read the 'How to use' section to know how to compile the code and use it.
UPDATE Version 1.1 solves some compilation problems that several users have reported. If you encounter any problem, feel free to send an email to email@example.com
If you are looking for the standalone version of jMetalCpp without AutoDock integration, you can download it here.