Well, firstly, why do you need to?
Secondly, Project Builder isn't exactly compatible with a build chain built on the gnu autotools. You can use makefiles with the "Legacy Makefile" target, or you can do the configuration manually (the point of configure is to check what facilities the OS provides for source which will run on multiple platforms - your PB project will only run on one, so you don't really need to test for the facilities using a script).