for an experiment I want to use native fragments. For this, I generated the necessary fragment files (3mers and 9mers).
Now I wanted to do a test run with AbinitioRelax and have the problem that nothing happens. I see the normal output from reading the database, but after that it seems to be "stuck"; nothing happens even after 13 hours. The protein has only 52 residues. If I run the same experiment with my normal fragments (generated by the fragment picker), it finishes after 2min. I can however use the native fragments in PyRosetta and can do predictions (using some starter code from the PyRosetta tutorials). What I noticed here is that the scores are huge, especially the fa_rep term, for full atom scoring somewhere around 55k. I tried different methods of preprocessing the PDB (idealizing and relaxing). With idealizing I have the same high scores, interestingly enough I find the native structure with the PyRosetta simulation. But it doesn't help for AbinitioRelax. When I shuffle that fragment file (this is the standard behavior of the struc_set_fragment_picker) AbinitioRelax works but with obviously very bad results. I tried a second protein in the mean time, same result.
Any idea what might cause this behaviour?
Thanks in advance!