I have been successfully following the protocol as per the paper “Small-molecule ligand docking into comparative models with Rosetta” to build the homology models of transporters using Rosetta 3.5. However, recently, after installing the latest version of rosetta :rosetta_2014.35.57232_bundle and tried to build the models using the protocol as mentioned in the paper (mentioned above) I could not build the models. The program is running without errors but could not fold the protein. I was wondering if i have to follow a different protocol for the latest version of rosetta? and how this issue could be fixed?