fa_atr Lennard-Jones attractive between atoms in different residues fa_rep Lennard-Jones repulsive between atoms in different residues fa_sol Lazaridis-Karplus solvation energy fa_intra_sol_xover4 Intra-residue Lazaridis-Karplus solvation energy lk_ball_wtd Asymmetric solvation energy fa_intra_rep Lennard-Jones repulsive between atoms in the same residue fa_elec Coulombic electrostatic potential with a distance-dependent dielectric pro_close Proline ring closure energy and energy of psi angle of preceding residue hbond_sr_bb Backbone-backbone hbonds close in primary sequence hbond_lr_bb Backbone-backbone hbonds distant in primary sequence hbond_bb_sc Sidechain-backbone hydrogen bond energy hbond_sc Sidechain-sidechain hydrogen bond energy dslf_fa13 Disulfide geometry potential rama_prepro Ramachandran preferences (with separate lookup tables for pre-proline positions and other positions) omega Omega dihedral in the backbone. A Harmonic constraint on planarity with standard deviation of ~6 deg. p_aa_pp Probability of amino acid, given torsion values for phi and psi fa_dun Internal energy of sidechain rotamers as derived from Dunbrack's statistics yhh_planarity A special torsional potential to keep the tyrosine hydroxyl in the plane of the aromatic ring ref Reference energy for each amino acid. Balances internal energy of amino acid terms. Plays role in design. METHOD_WEIGHTS Not an energy term itself, but the parameters for each amino acid used by the ref energy term.
I read the ref2015 score.
I use the ddg_monomer with ref 2015
① some items are not found, such as fa_elec , omega, rama_prepro.
② In addition, I can not understand some result，
hbond_sc show a -1.165 value (more negative more stable?)
tryptophan is hydrophobic, I can not undestand how it can contribute stability due to the hbond_sc
③ If I want to introduce h-bond to improve the stability, which item of the score that should be concerened ( the sum of hbond_sr_bb，hbond_lr_bb，hbond_bb_sc and hbond_sc?)
Regarding ddg_monomer application, it uses a slightly different way of specifying the scorefunction: -ddg::weight_file and -ddg::minimization_scorefunction -- I'd double check your command line to see what you've specified.
For tryptophan, it's hydrophobic because most of it is large and greasy, but it does have an N-H group in the sidechain which can make hydrogen bonds. An hbond_sc of -1.165 does indeed mean that there's a favorable sidechain hydrogen bond which is formed due to the mutation.
If you're introducing hydrogen bonds, it will show up in one of those terms. But you're less likely to see it in hbond_sr_bb and hbond_lr_bb which concern themselves with the backbone-backbone hydrogen bonds. Those will likely only change if you have a somewhat significant backbone rearrangment due to the mutation. You're more likely to see changes in hbond_bb_sc (where the mutated sidechain adds/changes a hydrogen bond to the backbone) and hbond_sc (where the mutated sidechain adds/changes a hydrogen bond to another sidechain).
Thanks a lot.
This is the minimization flag
-ddg::iterations 50 # 50 is the recommended number of iterations
-ddg::local_opt_only true # repack the residues in an 8 Angstrom shell around the site of the point mutation
-ddg::mean true #
-ddg::min false #
-database /media/G/rosetta_src/main/database #the full oath to the database is required
-in::file::fullatom # read the input PDB file as a fullatom structure
-fa_max_dis 9.0 # optional -- if not given, the default value of 9.0 Angstroms is used.
-ddg::output_silent true # write output to a silent file
This is the ddg_monomer flag, I check the log file, ref2015 was uesd
② The hbond_sc of A196I and A247V were 0.561 and -0.477, respectively. I and V are hydrophobic. It mean h-bond beweent the residue that surrounding 196I/247V and other residue was changed?