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 nov16 score function page here.
For most protocols (those that use getScoreFunction to set the protocol score function), the flag -gen_potential or simply -beta (which will always load the latest beta energy function) will load this version of the beta energy function.
For RosettaScripts protocols, the flag -gen_potential or -beta must be provided, and the following scorefunction declaration must be made:
<ScoreFunction name="beta" weights="beta_genpot"/> or <ScoreFunction name="beta" weights="beta"/>
An alternate atom typing scheme has been introduced. An alternate param file generation app, scripts/python/public/generic_potential/mol2genparams.py has been added to handle parameter generation with the new atom typing. NOTE: this new typing is completely separate from protein atom typing. Fore more information how thse atom types are defined and how this works, see here.
A generalized torsion term called "gen_bonded", a component of the generalized energy function, is defined according to the atom types and bond types at the torsion axis. It uses the common functional form used in regular force field, representing torsional preference as a series of cosine functions up to 4-th order. The parameters associated with the term can be found from the file located at the Rosetta database: database/scoring/score_functions/generic_potential/generic_bonded.round6p.txt
A new ligand docking protocol has been added, GALigandDock, that takes advantage of this new generic potential. It combines fast scoring on a precomputed grid with a genetic algorithm to allow very accurate ligand docking in 3-10 CPU minutes total per target (fixed sidechain) or 10-30 CPU minutes total (flexible sidechain).
Whole process preparing for GALigandDock runs starting from SMILES string or a mol2 file and assigning proper Generalized atom types through mol2genparams.py can be found here.