InterfaceAnalyzer total score = 0.000

[Anonymous]

I am trying to analyse a binding interface using Interfaceanalyzer. I minimized the complex using CHARMM and Rosetta and changed the residue numbering in the CHARMM minimized file to be ‘pose-numbered’ i.e. start from 1 for each chain without any insertion codes. I also removed the hydrogens from the CHARMM minimized file so that Rosetta can fill its own hydrogen numberings. Both the pdb files are attached. When I use Interfaceanalyzer, I obtained a total score of 0.000 for the Rosetta minimized file while a score of 600 (along with additional metrics) for the CHARMM minimized file. 

I use the following flags

-in:file:s ep1de40_ros.pdb

-interface BA_C

-compute_packstat=1

-out:file:score_only interface_out.out

 

The results for both the files are given below.

SEQUENCE: 

SCORE: total_score complex_normalized           dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA_int dSASA_polar delta_unsatHbonds dslf_fa13    fa_atr    fa_dun   fa_elec fa_intra_rep fa_intra_sol_xover4              fa_rep              fa_sol hbond_E_fraction hbond_bb_sc hbond_lr_bb    hbond_sc hbond_sr_bb hbonds_int lk_ball_wtd    nres_all    nres_int       omega     p_aa_pp    packstat per_residue_energy_int pro_close rama_prepro         ref    sc_value side1_normalized side1_score side2_normalized side2_score yhh_planarity description 

SCORE:     505.114              1.315              0.000              0.000      -60.679                 -1.942      1534.975  3125.223    1590.248            22.000     0.000 -2218.291  1054.073  -698.196        4.961              74.195             311.952            1489.409            0.279     -67.015    -123.755     -42.379     -49.359     21.000      11.299     384.000     114.000     194.998     -36.805       0.716                  2.315   162.541     248.044     189.440       0.699            1.602      92.913            3.054     171.008         0.000 ep1de40_cha_pose_0001

 

SEQUENCE: 

SCORE: total_score complex_normalized           dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA_int dSASA_polar delta_unsatHbonds hbond_E_fraction hbonds_int   nres_all   nres_int   packstat per_residue_energy_int               sc_value side1_normalized side1_score side2_normalized side2_score description 

SCORE:       0.000             -1.578              0.000              0.000      -69.655                 -2.456      1287.984  2835.958    1547.974            19.000            0.265     18.000    384.000    105.000      0.586                 -1.230                  0.696           -1.413     -77.699           -1.028     -51.405 ep1de40_ros_0001

 

I am doing this analysis to get the metrics which were obtained in the article: RosettaAntibodyDesign (RAbD): A general framework for computational antibody design (2018). While both the files give me values for dG_separated, the total_score (Total E, Opt-E in RAbD) is being given for only the CHARMM minimized file. Kindly assist me on this. 

Thanks 

[Anonymous]

For the InterfaceAnalyzer application, if you don’t do repack_separated=true, there is no guarantee that the whole complex is scored as IAM (InterfaceAnalyzerMover) does some internal copying.  In the paper, repack_separated was true.  That said, IAM is correctly reporting the interface energy.  If you add the option to repack after separation and you still don’t get a score, I would use the score application to get the total score.  You could also call IAM through RosettaScripts and use the ScoreMover to make sure a score is output. 

[Anonymous]

I used pack_separated=true but got the same total score of 0.000 for the Rosetta minimized file. So the total score from /main/source/bin/score_jd2.default.linuxgccrelease should give me the same value as the total score from InterfaceAnalyzer?

Thanks for the reply.

[Anonymous]

Yes, it will.  In the meantime, I’ll see what is going on with IAM in terms of the total score – it would definitely be nice if all the scoring was there.  RAbD used IAM internally to do everything, so that didn’t come up. 

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