I am using FloppyTail in Rosetta 3.2. After the first stage, the centroid modelling, there was really an expected folding in my designated tail region. However, my problem was that the protein containing floppy tail dissociated from original protein complex significantly, but the other components were still well organized as previous. Also, the second stage, fullatom modeling, could not correct it. How could I deal with it?
I thought those input start and stop residues positions were right, fragment file was also provided.
Thanks very much.