Reply To: Why do non proten ligands get a very high score in kinematic loop modeling/ in general?

[Anonymous]

High scores are usually the result of clashes. I’m guessing you have a high fa_intra_rep score for the ligand. Rosetta is almost certainly not relaxing the ligand, so any small things about the input Rosetta doesn’t like will stay that way.

Does your score result have the per-residue and per-score section that looks something like what’s below, which you can use to diagnose which term is causing the large score? (fa_intra_rep is the 5th column in this case).

# All scores below are weighted scores, not raw scores.
#BEGIN_POSE_ENERGIES_TABLE UBQ_E2_0001.pdb
label 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 atom_pair_constraint rama omega fa_dun p_aa_pp ref total
weights 0.8 0.44 0.65 0.004 1 0.49 0.585 1.17 1.17 1.1 0.5 2 5 5 50 0.2 0.5 0.56 0.32 1 NA
pose -820.344 239.487 403.65 2.10127 27.0666 -12.5863 -47.5282 -58.9692 -16.5835 -4.65349 0 0 0 0 376.642 -3.95454 87.7306 445.125 -19.2129 -52.33 545.64
SER_p:NtermProteinFull_1 -2.37325 0.158463 1.98733 0.00286597 0 0.00173929 0 0 0 0 0 0 0 0 0 0 0.303073 4.67488 0 -0.37 4.38511
GLN_2 -2.83504 1.43855 1.52157 0.00454749 0 -0.00514894 0 0 0 0 0 0 0 0 0 -0.204038 0.0608883 4.71246 -0.122122 -0.97 3.60167
LYS_3 -2.70773 0.480922 1.32955 0.00670788 0 0.00688822 0 0 0 0 0 0 0 0 0 -0.14769 2.02297e-05 3.46405 -0.041184 -0.65 1.74154
ALA_4 -3.03849 0.119461 1.42765 0.000817063 0 0 0 0 0 0 0 0 0 0 0 -0.128825 0.000990234 0 -0.149645 0.16 -1.60804