I've just fresh installed the last rosetta version (2014.35) and can't be able to appropriately run protocols that used to work in previous versions. It doesn't matter if I run single or mpi binaries. Loopmodel is running pretty well without warnings, however, the output pdbs are just linear aa sequences. Flags file is in attachment but I could share the entire directory by email. I woulld appreciate if someone who has experienced such problem could share the solution.