Add Custom Labels to NLTK Information Extractor
Once you have your own lists of named entities, and you're only interested in extracting the relations, I believe there are simpler solutions (although I never tried relation extraction in NLTK, so I might be wrong):


ReVerb - a tool written in Java. Once it produces the results, you can simply keep the rows, where your labels are present as objects of the relation.
OpenIE - the successor of ReVerb (also written in Java). The authors claim better perfomance, and the output might be more informative.
IEPY - a relation extraction tool in Python. You should be able to provide your own labels/named entities using gazetees.
MITIE - this library has bindings in Python, and it offers relation extraction functionality.