fixbb in Rosetta 3.4 to perform fixed BB design using damped LJ potential (by specifying parameter
-soft_rep_design). But I noticed that the final score reported by fixbb seemed to be calculated using default weights. (I got to know this by using
score_jd2 to recalc the score for deboys using default weights and damped weights and compare them to the score reported by fixbb.) Does this mean my design was really done using damped LJ? Or the parameter
-soft_rep_design was ignored and the design was done by using default weights?
It also seems the default weights is "score12", not "standard" (as the manual claims). What is the background story of these two score weights? Which corresponds to the "HardRep" weights?
Also, what is the difference between soft_rep and soft_rep_design? If one wants to do fixbb with damped rep LJ potential, which should one use?