I am recording the positions of all atoms before I run a Rosetta protocol + external software perturbations, and using these positions to "reset" the system after the protocals have completed. The score is computed before and after the protocols, and after resetting the system. I noticed resetting causes a large increase in the score (-1000 to 25000).
Looking at the score by residue, the culprit was pro_close for Prolines...
-My first guess is that this is an improper ring angle, except that this structure was a starting structure in Rosetta.
-I am fairly sure all atoms are in place, as I have visualized the structure and compared atom lists in outputted PDBs.
-The pro_close term is the only large term in the score.
Are there some other structural changes of residues that occur with repacking during a Rosetta protocol? (e.g. HIS_D to HIS_E)