rdk
The fact that you are not root shouldn't be a problem. I just tried o build it as non-root on the same version of ubuntu and java and it worked....
Closing an old issue. @iitb33 if you still have problems running P2Rank let me know.
In the meantime this has been solved on develop branch by using custom fork of biojava (biojava-structure-6.1.0-rdk1).
Fixed in 2.4.2 release. Aslo in the meantime fixed in BioJava 7.1