When I am looking the energy terms of the fixbb, I find that the rosetta 3.3 has terms as below
> hbond_sr_bb *= 0.5
> p_aa_pp *= 0.5
> rama = 0.2
> omega = 0.5
But 2.3 has only 11 terms.
bk_tot The total score using the design energy function. Lower is better.
fa_atr The attractive portion of the Lennard-Jones? potential. Rewards close contacts.
fa_rep Lennard-Jones repulsive term. Penalizes overlaps.
fa_sol Lazaridis-Karplus solvation model. Penalizes buried polars.
fa_dun Internal energy of sidechain rotamers as derived from Dunbrack's statistics.
fa_intrares Intra-residue clashes.
fa_pair Statistics based paird term. Favors salt bridges.
fa_prob Probabilistic term: P(aa
hb_sc Sidechain-sidechain and sidechain-backbone hydrogen bond energy.
hb_srbb Backbone-backbone hydrogen bonds close in primary sequence.
hb_lrbb Backbone-backbone hydrogen bonds distant in primary sequence.
Also, I am confused that whether bk_tot is an energy term in rosetta2.3. It seems to me, bt_tot is the sum of packing energy. Thank you for your kindly help!