Apparently, there's no free software that i know of. As you have mentioned that you only have P-P interaction information only, I suggest you to try the following method.

1) Target that active site ( Since i have used schrodinger , it is know as making GRID around the P-P binding site)

2) Carry out a fragment based screening Initially. (Docking)

3) Choose the fragment accordingly and then screen the database having similar pharmacophore.

4) Simulate the P-P complex.

5) Simulate the P-P-Ligand complex

This will give u a fair idea if the molecule you have selected is breaking the interaction or not.

The following webservers available for pharmacophore modeling.

Pharmagist: http://bioinfo3d.cs.tau.ac.il/PharmaGist

ZINCPharmer: http://zincpharmer.csb.pitt.edu/

Pharmit: http://pharmit.csb.pitt.edu/

Commercial softwares:

Discovery Studio: http://accelrys.com/products/collaborative-science/biovia-discovery-studio/

LigandScout: http://www.inteligand.com/ligandscout/

Phase: www.schrodinger.com

MOE - Pharmacophore Discovery: https://www.chemcomp.com/MOE-Pharmacophore_Discovery.htm

ICM-Chemist: http://www.molsoft.com/icm-chemist.html

https://www.researchgate.net/publication/279303233_Surfing_the_Protein-Protein_Interaction_Surface_Using_Docking_Methods_Application_to_the_Design_of_PPI_Inhibitors

On that article, there are list some of web servers that can generate protein-protein interaction. You can choose one of them.

Pharmagist is an excellent server -free and i have used several times

http://bioinfo3d.cs.tau.ac.il/PharmaGist