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

[Anonymous]

hi smlewis,

Actually it is fa_rep term that is high (please see below). In this case I am simply trying to score green fluorescent protein (1EMA.pdb). LG1 score is 245 while the whole structure score is 643.

I attached the .mol2 file for the chromophore (generated using openbabel) and the .params file (generated using molfile_to_params.py).
I also uploaded the input pdb for scoring (which includes LG1 instead of the CRO; coordinated of which are from the pdb file generated with LG.params)

Thanks a lot for your help

# All scores below are weighted scores, not raw scores.
#BEGIN_POSE_ENERGIES_TABLE 1EM1_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 rama omega fa_dun p_aa_pp ref linear_chainbreak overlap_chainbreak 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 0.2 0.5 0.56 0.32 1 1.33333 1 NA
pose -863.018 789.902 433.068 2.50203 61.6793 -20.4745 -17.9809 -145.897 -16.7595 -18.4937 0 0 0 0 2.35112 41.8995 458.407 -19.677 -43.73 0 0 643.778
SER_p:NtermProteinFull_1 -1.41494 0.134777 1.2167 0.00901941 0 -0.0354852 0 0 0 0 0 0 0 0 0 0.0078096 1.24065 0 -0.37 0 0 0.78854
LYS_2 -3.49071 4.74493 3.08823 0.00542008 0 -0.484169 0 0 -0.551881 -0.253388 0 0 0 0 0.972774 0.120974 9.20326 -0.058382 -0.65 0 0 12.6471
.
.
GLY_224 -1.0332 0.148119 0.513931 1.58146e-05 0 0 0 0 0 0 0 0 0 0 -0.355812 0.00998178 0 -0.803254 -0.17 0 0 -1.69022
ILE_p:CtermProteinFull_225 -3.25505 15.5117 1.38385 0.018914 0 0 0 0 -0.213718 0 0 0 0 0 0 0 4.90175 0 0.24 0 0 18.5875
LG1_226 -13.0798 250.61 8.83978 0.028532 0 0 0 0 0 -0.996807 0 0 0 0 0 0 0 0 0 0 0 245.402
#END_POSE_ENERGIES_TABLE 1EMA_CRO_to_LG1_0001.pdb