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
| Attachment | Size |
|---|---|
 ep1de40_cha_pose.pdb | 231.38 KB |
| ep1de40_ros.pdb | 506.78 KB |
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.
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.
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.