I am running the script for protein design downloaded from http://pyrosetta.org/scripts.html.
It makes design of the last 10 aa of the protein while the rest of the protein remains unchanged.
When I calculated 100 decoys, in 99 cases I obtained the same sequence of the designed fragment (different from the native one).
When I allowed for changes of sidechains rotamers in the rest of the protein I also obtained sets of the same decoys.
It is strange... Is it ok???
Is it possible to monitor how the sequence is changing during design?