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Further Terms

This section supplements the main Score Types section with other energy terms available in Rosetta.

Context-independent two-body energy terms

Short-ranged context-independent two-body score terms

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.

pba Membrane all atom terms

fa_mbenv                                   Depth-dependent reference term
fa_mbsolv                                  Burial + depth dependent term

Split out fa_elec for RNA

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

Carbon hydrogen bonds

ch_bond                                    
ch_bond_bb_bb
ch_bond_sc_sc
ch_bond_bb_sc

Proline closure energy

rama2b
vdw                                        Centroid
cenpack                                    Centroid
cenpack_smooth                             fpd smooth cenpack
cen_hb                                     fpd centroid bb hbonding
hybrid_vdw                                 Hybrid centroid+fa

Gaussian overlap

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

RNA terms

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

High-resolution RNA terms

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 constraints-based torsional potentials

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

All the orbitals scoretypes

orbitals_hpol_bb
pci_cation_pi
pci_pi_pi
pci_salt_bridge
pci_hbond

Context-dependent two-body energy terms

Short-ranged context-independent two-body score terms

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

Protein-protein interface scores

interface_dd_pair

Geometric solvation

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

Centroid rotamer pair, P(r,ang,dih|aa)

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

Sucker atom energy

suck

RNA low-resolution terms

rna_rg                                     Radius of gyration for RNA

Nucleotide resolution thermodynamics

loop_close                                 Loop closure terms - attempting to model full RNA folding free energy

FACTS solvation model

facts_elec
facts_solv
facts_sasa

Centroid inter-chain one-body (docking) scores

interchain_pair
interchain_vdw

Other energy terms

Miscellaneous

gb_elec

Full-atom disulfide terms

dslf_cbs_ds                                Replaced by dslf_fa13 in talaris2013

Centroid disulfide terms

dslfc_cen_dst
dslfc_cb_dst
dslfc_ang
dslfc_cb_dih
dslfc_bb_dih

Disulfide matching terms

dslfc_rot
dslfc_trans
dslfc_RT

Constraint terms

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

Miscellaneous

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 potential

PB_elec

Centroid whole structure energies

Centroid whole structure energies

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

Secondary structure scores

natbias_ss
natbias_hs
natbias_hh
natbias_stwist

Amino acid composition score

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

Additional score terms

Miscellaneous

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

Centroid interchain one-body (docking) scores

interchain_env
interchain_contact

Miscellaneous

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

Neighbor Vector solvation approximation

neigh_vect
neigh_count
neigh_vect_raw

Symmetry bonus

symE_bonus

Implicit ligand interactions (symmetry)

sym_lig

Packing score energy

pack_stat

Model-quality metrics.

rms                                        All-heavy-atom RMSD to the native structure

ResidueConstraint terms

res_type_constraint

Residue Type linking constraint

res_type_linking_constraint

PocketConstraint terms

pocket_constraint

BackboneStubConstraint terms

backbone_stub_constraint
backbone_stub_linear_constraint
surface
p_aa
unfolded

Fit-to-density score terms

elec_dens_fast
elec_dens_window
elec_dens_whole_structure_ca
elec_dens_whole_structure_allatom
elec_dens_atomwise

Patterson correlation score terms

patterson_cc

Crystallographic ML target

xtal_ml
xtal_rwork
xtal_rfree
hpatch

Membrane environment smooth

Menv_smooth

See Also