printing our per-residue energies including H-bonding energies

[Anonymous]

Hi all

Could anyone help me out in figuring out a way for printing out per-residue energies including the “hydrogen bond energies” using Rosetta 3.4. It sounds that the per residue energies obtained at the end of the annotated PDB files doesn’t includes the hydrogen bond energies, as Rosetta stores H-bonding energies only on a per-pose basis. This results in inconsistencies between the sum of per residue energy and the total energy reported by Rosetta.

Thanking in advance

Regards,
Vijayan.R

[Anonymous]

Hi Vijayan,
You can use per_residue_energies.linuxgccrelease which print the energies per residue as

SCORE: pose_id fa_atr fa_rep fa_sol fa_intra_rep 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 rama omega fa_dun p_aa_pp ref score description
SCORE: 1.pdb -1.875 2.173 0.655 0.011 1.471 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.039 0.000 0.290 2.765 residue_1
SCORE: 1.pdb -3.324 0.592 0.962 0.001 1.487 0.000 0.000 -0.831 0.000 0.000 0.000 0.000 0.000 0.000 -0.289 0.762 0.395 -0.562 0.020 -0.787 residue_2

Is that what you’re looking for?

[Anonymous]

per_residue_energies is an unreleased pilot app, so wouldn’t be available unless you have the internal developers source. I don’t believe there’s a way to access that information in the release version without recompiling.

A quick fix is to edit score_jd2 to insert the following lines to the file (not-tested: line numbers given for reference, and might not be exact.), recompile, and then run the score_jd2 application on your structures with the -out:pdb option. This should have the backbone H bonding breakdown in the output PDB.:

00029 #include <core/scoring/Energies.hh>
00030 #include <core/scoring/ScoreFunction.hh>
+++ #include <core/scoring/methods/EnergyMethodOptions.hh>
+++ #include <core/scoring/hbonds/HBondOptions.hh>
00031 #include <core/scoring/ScoreFunctionFactory.hh>
00032 #include <basic/options/option.hh>

…

00147 sfxn_->set_weight( core::scoring::linear_chainbreak, 4.0/3.0 );
00148 sfxn_->set_weight( core::scoring::overlap_chainbreak, 1.0 );
+++ core::scoring::methods::EnergyMethodOptionsOP emopts( new core::scoring::methods::EnergyMethodOptions( scorefxn->energy_method_options() ) );
+++ emopts->hbond_options().decompose_bb_hb_into_pair_energies( true );;
+++ scorefxn->set_energy_method_options( *emopts );
00149
00150 if ( ! skip_scoring_ ) {
00151 (*sfxn_)( pose );
00152 }
00153 }


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