I am quite new to Rosetta and currently using the loopmodel application to remodel and refine some loops. Everything seems to be working fine. However, upon evaluation of the predicted structures I noticed the absurdly high total energies calculated for the modeled structures. When recalculated with the score_jd2 app, I get an energy of 793748.772 for the model and -1069.460 for the native structure.
What's going on here? I'm using Rosetta 3.2 and the following options with loopmodel:
-ex1 -ex2 -extrachi_cutoff 0
-loops:neighbor_dist 6.0 -nstruct 100
Any ideas for a beginner?
Thank you in advance!