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The hbond for REF2015

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The hbond for REF2015


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,

such as 

description total fa_atr fa_rep fa_sol pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih fa_dun p_aa_pp ref
A91W -5.966 -23.381 14.088 1.447 0 0 0 0 0 -1.165 0 0 0 0 2.52 -0.734 1.261


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?)

Post Situation: 
Mon, 2022-06-06 06:07

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).


Mon, 2022-06-06 08:10

Thanks a lot.

-fa_max_dis 9.0 
-ddg::harmonic_ca_tether 0.5 
-ddg::constraint_weight 1.0 
-ddg::out_pdb_prefix min_cst_0.5 
-ddg::sc_min_only false 
-database /media/G/rosetta_src/main/database/ 
This is the minimization flag


-ddg::mut_file mut.mutfile 
-ddg:weight_file soft_rep_design 
-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::min_cst false
-ddg::mean true #
-ddg::min false # 
-ddg::sc_min_only false 
-ddg::ramp_repulsive  false
-ddg::opt_radius 8.0
-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? 

Mon, 2022-06-06 23:15