fa_atr lennard-jones attractive
fa_rep lennard-jones repulsive
fa_sol lazaridis-jarplus solvation energy
fa_intra_rep lennard-jones repulsive between atoms in the same residue
fa_pair statistics based pair term, favors salt bridges
fa_plane pi-pi interaction between aromatic groups, by default = 0
fa_dun internal energy of sidechain rotamers as derived from Dunbrack's statistics
ref reference energy for each amino acid
hbond_lr_bb backbone-backbone hbonds distant in primary sequence
hbond_sr_bb backbone-backbone hbonds close in primary sequence
hbond_bb_sc sidechain-backbone hydrogen bond energy
hbond_sc sidechain-sidechain hydrogen bond energy
p_aa_pp Probability of amino acid at phipsi
dslf_ss_dst distance score in current disulfide
dslf_cs_ang csangles score in current disulfide
dslf_ss_dih dihedral score in current disulfide
dslf_ca_dih ca dihedral score in current disulfide
pro_close proline ring closure energy
rna_torsion RNA torsional potential.
geom_sol Geometric Solvation energy for polar atoms
ch_bond Carbon hydrogen bonds
lk_nonpolar Lazaridis-karplus solvation energy, over nonpolar atoms
hack_elec_rna_phos_phos Simple electrostatic repulsion term between phosphates
rna_rg Radius of gyration for RNA
rna_vdw Low resolution clash check for RNA
rna_base_backbone Bases to 2'-OH, phosphates, etc.
rna_backbone_backbone 2'-OH to 2'-OH, phosphates, etc.
rna_repulsive Mainly phosphate-phosphate repulsion
rna_base_pair_pairwise Base-base interactions (Watson-Crick and non-Watson-Crick)
rna_base_pair Base-base interactions (Watson-Crick and non-Watson-Crick)
rna_base_axis Force base normals to be parallel
rna_base_stagger Force base pairs to be in same plane
rna_base_stack Stacking interactions
rna_base_stack_axis Stacking interactions should involve parallel bases.
atom_pair_constraint Harmonic constraints between atoms involved in Watson-Crick base
pairs specified by the user in the params file
rms all-heavy-atom RMSD to the native structure
