Energy Terms In Rosetta 3

We will intoduce couple of typical Rosetta 3 weights files in this page to let you have a basic idea about energy terms in Rosetta 3.

Standard Weights File

Score12 is the most common used score file in Rosetta 3. It includes the standard.wts and score12.wts_patch. We will emphasize the energy terms used in these files here.

Energy terms using in standard.wts

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

Energy Terms using in score12.wts_patch

rama                                       ramachandran preferences
omega                                      omega dihedral in the backbone

Energy Terms Using in RNA Applications

Here, we list the Energy terms used in RNA denovo and design applications. Energy terms we have introduced above will not be repeat again.

Energy Terms using in rna high resolution weights files

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

Energy Terms using in rna low resolution weights files

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

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