Note: this parameterization has been superseded by beta_nov16.
An overview of this energy function optimization effort is available here.
For information on the previous set of updates to this score function, see the beta july15 score function page here.
For benchmark results of protocols, see here.
For most protocols (those that use getScoreFunction to set the protocol score function), the flag -beta_nov15 will load this version of the beta energy function.
For RosettaScripts protocols, the flag -beta_nov15 must be provided, and the following scorefunction declaration must be made:
Optimization followed the same scheme as beta_july15, and used that function as a starting point. However, in addition to optimizing several new parameters, modifications were made to the target function used during optimization:
Electrostatics & partial charges (fa_elec)
In this optimization we considered optimizing individual atomic partial charges. To reduce the number of parameters as well as maintain the overall charge of the molecules, we used the following scheme:
More importantly, an issue where the count-pair logic in Rosetta was splitting dipoles has been corrected. This is fixed by specifying a "representative atom" for each atom that is used for countpair purposes. This is specified using the flag -elec_representative_cp or -elec_representative_cp_flip which uses the minimum or maximum length within each group, respectively, when determining what count pair multiplier to apply. The beta_nov15 energy function uses the maximum length (-elec_representative_cp_flip).
Hatr (fa_atr for hydrogens)
Attractive energies were enabled for hydrogen atoms (-fa_Hatr), and LJ parameters were refit. Due to the significant changes this induces in the LJ parameters, this refitting was initially guided entirely by agreement to biophysical data using small molecule liquid simulations, then using the complete target function.
Torsion library updates (fa_dun/rama_prepro/p_aa_pp)
Several torsional updates were included before optimization:
Bondlength, bondangle and planarity restraints (cart_bonded)
Bondlength and bond angle parameters were updated in several ways. Initially, several errors in the cart_bonded parameter file were corrected:
Secondly, optimization was carried out with the spring constants used in cart bonded. All angles, lengths, and torsions were divided into 130 "classes", and a scaling factor was calculated for each class. These scaling factors were optimized using two criteria:
Several minor modifications were made to the energy function as well: