This section supplements the main Score Types section with other energy terms available in Rosetta.
fa_intra_atr
fa_intra_sol
fa_intra_RNA_base_phos_atr RNA-specific score term
fa_intra_RNA_base_phos_rep RNA-specific score term
fa_intra_RNA_base_phos_sol RNA-specific score term
lk_hack
lk_ball
lk_ball_wtd
lk_ball_iso
coarse_fa_atr
coarse_fa_rep
coarse_fa_sol
coarse_beadlj
mm_lj_intra_rep
mm_lj_intra_atr
mm_lj_inter_rep
mm_lj_inter_atr
mm_twist
mm_bend Deviation of bond angles from the mean
mm_stretch
lk_costheta
lk_polar
lk_nonpolar Lazaridis-Karplus solvation energy, over nonpolar atoms
lk_polar_intra_RNA RNA-specific score term
lk_nonpolar_intra_RNA RNA-specific score term
fa_elec_bb_bb
fa_elec_bb_sc
fa_elec_sc_sc
h2o_hbond
dna_dr
dna_bp
dna_bs
peptide_bond
pcs Pseudo-contact Shift energy
pcs2 Pseudo-contact Shift energy version 2. This will replace pcs by the end of 2010
fastsaxs Fastsaxs agreement using formulation of Stovgaard et al. [1]
saxs_score Centroid SAXS asessment
saxs_cen_score
saxs_fa_score Full-atom SAXS score
pddf_score Score based on pairwise distance distribution function
cen_pair_motifs Motif score to determine packing in the protein core. Applied to each residue
[1] Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models, Stovgaard et al., BMC Bioinformatics. 2010; 11:429.
fa_mbenv Depth-dependent reference term
fa_mbsolv Burial + depth dependent term
fa_elec_rna_phos_phos fa_elec between rna phosphates only, needed to prevent unrealistic phos-phos interactions
fa_elec_rna_phos_sugr
fa_elec_rna_phos_base
fa_elec_rna_sugr_sugr
fa_elec_rna_sugr_base
fa_elec_rna_base_base
fa_elec_rna_phos_phos_fast
fa_elec_rna_phos_sugr_fast
fa_elec_rna_phos_base_fast
fa_elec_rna_sugr_sugr_fast
fa_elec_rna_sugr_base_fast
fa_elec_rna_base_base_fast
fa_elec_aro_aro
fa_elec_aro_all
hack_aro
rna_fa_atr_base
rna_fa_rep_base
rna_data_backbone Using chemical accessibility data for RNA
ch_bond
ch_bond_bb_bb
ch_bond_sc_sc
ch_bond_bb_sc
rama2b
vdw Centroid
cenpack Centroid
cenpack_smooth fpd smooth cenpack
cen_hb fpd centroid bb hbonding
hybrid_vdw Hybrid centroid+fa
gauss
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_axis_pairwise Force base normals to be parallel
rna_base_stagger_pairwise Force base pairs to be in same plane
rna_base_stack_pairwise Stacking interactions
rna_base_stack_axis_pairwise Stacking interactions should involve parallel bases
rna_data_base Using chemical accessibility data for RNA
This is a filtered version of the pairwise RNA low-resolution terms above, disallows a base edge to form more than one base pair, and disallows two bases to both stack and pair.
This is not really pair-wise but is calculated in a finalize_energy step at the end of a 2-body score function.
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
rna_mg Knowledge-based term for mg(2+)RNA interactions for use in low-resolution modeling
rna_mg_rep Ad hoc, empirically validated term to prevent uncommon mg(2+)atom interactions
rna_mg_indirect Knowledge-based term for mg(2+)RNA interactions for use in low-resolution modeling
rna_torsion RNA torsional potential
rna_sugar_close Constraints to keep RNA sugar closed, and with reasonably ideal geometry
fa_stack Stacking interaction modeled as pairwise atom-atom interactions
fa_stack_aro
stack_elec Distance dependent dielectric between base atoms (attenuated parallel to plane)
stack_elec_base_base
stack_elec_base_bb
dna_bb_torsion
dna_sugar_close
dna_base_distance
geom_sol_fast Context independent version. Currently tested only for RNA case
geom_sol_fast_intra_RNA RNA specific score term
fa_cust_pair_dist Custom short range two-body
custom_atom_pair
orbitals_hpol_bb
pci_cation_pi
pci_pi_pi
pci_salt_bridge
pci_hbond
fa_pair_aro_aro
fa_pair_aro_pol
fa_pair_pol_pol
hbond_sr_bb_sc
hbond_lr_bb_sc
hbond_intra Currently effects only RNA
interface_dd_pair
geom_sol Geometric solvation energy for polar atoms
geom_sol_intra_RNA RNA-specific score term
occ_sol_fitted
occ_sol_fitted_onebody
occ_sol_exact
cen_rot_pair P(r|aa)
cen_rot_pair_ang P(ang|r,aa)
cen_rot_pair_dih P(dih|r,aa)
pair Centroid
cen_pair_smooth fpd smooth centroid pair
Mpair
suck
rna_rg Radius of gyration for RNA
loop_close Loop closure terms - attempting to model full RNA folding free energy
facts_elec
facts_solv
facts_sasa
interchain_pair
interchain_vdw
gb_elec
dslf_cbs_ds Replaced by dslf_fa13 in talaris2013
dslfc_cen_dst
dslfc_cb_dst
dslfc_ang
dslfc_cb_dih
dslfc_bb_dih
dslfc_rot
dslfc_trans
dslfc_RT
atom_pair_constraint Harmonic constraints between atoms involved in Watson-Crick base pairs specified by the user in the params file
constant_constraint
coordinate_constraint
angle_constraint
dihedral_constraint
big_bin_constraint
dunbrack_constraint
site_constraint
metalhash_constraint Rigid body, metal binding constraints for centroid mode
rna_bond_geometry Deviations from ideal geometry
fa_dun_dev
fa_dun_rot
fa_dun_semi
dna_chi
p_aa_pp_offset
yhh_planarity
h2o_intra
ref_nc
seqdep_ref
nmer_ref
nmer_pssm
nmer_svm
envsmooth
e_pH
rna_bulge
mg_ref Chemical potential for mg(2+) ('reference weight' in Rosetta terminology)
free_suite Bonus for virtualizing RNA suite
free_2HOprime Bonus for virtualizing RNA 2'-OH
intermol Cost of instantiating a chain form 1 M std state
special_rot
other_pose In preparation for multi-pose stuff
PB_elec
cen_env_smooth fpd smooth centroid env
cbeta_smooth fpd smooth cbeta
cen_pair_motif_degree Determines packing in protein core. Only counts the best packed residue over a region. Whole-strucuture version of cen_pair_motifs
cen_rot_env
cen_rot_dun
env
cbeta
DFIRE
Menv
Mcbeta
Menv_non_helix
Menv_termini
Menv_tm_proj
Mlipo
rg Radius of gyration
rg_local Radius of gyration for repeat proteins
co Contact order
hs_pair
ss_pair
rsigma
sheet
burial Informatic burial prediction
abego Informatic torsion-bin prediction
natbias_ss
natbias_hs
natbias_hh
natbias_stwist
aa_cmp
dock_ens_conf Conformer reference energies for docking
csa NMR chemical shift anisotropy energy
dc NMR dipolar coupling energy
rdc NMR residual dipolar coupling energy
rdc_segments Fit alignment on multiple segments independently
rdc_rohl
holes
holes_decoy
holes_resl
holes_min
holes_min_mean
rna_chem_shift RNA NMR chemical shift pseudo-energy term
dab_sasa Classic 1.4A probe solvant accessible surface area
dab_sev Solvent excluded volume - volume of atoms inflated by 1.4A
sa Nonpolar contribution in GBSA
d2h_sa Correlation between SASA and hydrogen exchange data
ProQM Membrane MQAP
ProQ MQAP
interchain_env
interchain_contact
chainbreak
linear_chainbreak
overlap_chainbreak
distance_chainbreak
dof_constraint
rama2b_offset
omega2b_offset
cart_bonded Cartesian bonded potential
cart_bonded_angle Cartesian bonded potential
cart_bonded_length Cartesian bonded potential
cart_bonded_torsion Cartesian bonded potential
total_score
neigh_vect
neigh_count
neigh_vect_raw
symE_bonus
sym_lig
pack_stat
rms All-heavy-atom RMSD to the native structure
res_type_constraint
res_type_linking_constraint
pocket_constraint
backbone_stub_constraint
backbone_stub_linear_constraint
surface
p_aa
unfolded
elec_dens_fast
elec_dens_window
elec_dens_whole_structure_ca
elec_dens_whole_structure_allatom
elec_dens_atomwise
patterson_cc
xtal_ml
xtal_rwork
xtal_rfree
hpatch
Menv_smooth