Hi,
I'm trying to analyze the smina scoring function and I can't understand one thing.
For example for first conformation our affinity equals -7.404037
but sum of terms from per-atom interaction term values output doesn't equal to this affinity.
atomid el pos gauss(o=0,_w=0.5,_c=8) gauss(o=3,_w=2,_c=8) repulsion(o=0,_c=8) hydrophobic(g=0.5,_b=1.5,_c=8) non_dir_h_bond(g=-0.7,_b=0,_c=8)
1 C <8.16176,8.08049,30.2923> -0.135554 -0.168733 2.92616e-05 -0 -0
4 N <8.74609,7.67115,29.009> -0.0985983 -0.209402 0.0175504 -0 -0.121284
17 C <6.94089,7.16091,30.5722> -0.0973932 -0.184389 0.0271909 -0 -0
32 C <7.76487,9.56007,30.2543> -0.219725 -0.165859 0.00526744 -0 -0
2 C <10.0961,7.45643,28.9114> -0.231113 -0.231126 0 -0 -0
6 C <10.5579,6.9212,27.578> -0.117098 -0.243291 0 -0.0660077 -0
3 O <10.865,7.57631,29.8598> -0.284881 -0.248721 0.33664 -0 -0.472098
5 H <8.12459,7.31968,28.2866> -0 -0 0 -0 -0
7 C <9.82724,5.61201,27.2586> -0.0452682 -0.266096 0.0325638 -0.0303372 -0
8 C <10.7609,4.39997,27.0938> -0.0961498 -0.321818 0.0256678 -0 -0
13 C <10.1051,3.32015,26.2364> -0.172398 -0.320341 0.0382658 -0 -0
9 N <12.0092,4.88929,26.3991> -0.191043 -0.29161 0.107565 -0 -0.420892
10 H <12.4795,5.64164,26.9155> -0 -0 0 -0 -0
11 H <11.7729,5.22314,25.4511> -0 -0 0 -0 -0
12 H <12.6811,4.12001,26.2713> -0 -0 0 -0 -0
14 O <9.08672,3.56361,25.5952> -0.178978 -0.27041 0.108214 -0 -0.266128
15 O <10.7205,2.12585,26.2183> -0.111642 -0.329835 0.835749 -0 -1.37809
16 H <11.6201,2.02748,26.6285> -0 -0 0 -0 -0
18 O <5.9942,7.53571,31.2735> -0.060993 -0.19048 0.178217 -0 -0.383228
19 N <6.98071,5.93482,29.9172> -0.0518313 -0.192581 0 -0 -0
21 C <6.06441,4.82845,30.2832> -0.0173473 -0.158894 0 -0 -0
20 H <7.90981,5.63629,29.6202> -0 -0 0 -0 -0
22 C <6.80086,3.48584,30.2161> -0.105538 -0.218489 0 -0.190403 -0
28 C <4.82459,4.9011,29.3587> -0.0356116 -0.164706 0.00652895 -0 -0
23 C <6.58779,2.4468,31.1423> -0.136762 -0.226482 0 -0.245611 -0
24 C <7.27689,1.23095,31.0428> -0.162749 -0.272191 0.0194631 -0.215073 -0
25 C <8.19388,1.02542,30.0187> -0.204484 -0.268503 0.0937594 -0.255744 -0
26 C <8.43436,2.04095,29.0974> -0.138953 -0.27358 0.0132743 -0.208421 -0
27 C <7.75491,3.26033,29.2031> -0.085303 -0.247237 0 -0.156435 -0
29 O <4.76601,5.51799,28.3047> -0.0376556 -0.117121 0 -0 -0
30 O <3.72974,4.27301,29.8761> -0.0138058 -0.153716 0.198861 -0 -0.408259
31 H <3.94816,3.939,30.7733> -0 -0 0 -0 -0
33 S <6.61932,9.89693,28.8874> -0.0916693 -0.116072 0.0210967 -0 -0
34 C <5.76874,11.3615,29.5618> -0.0631233 -0.118371 5.44132e-06 -0 -0
35 C <6.06308,12.5634,28.7051> -0.0303411 -0.127089 0 -0.0143201 -0
36 C <5.13976,12.9826,27.7365> -1.11563e-05 -0.100721 0 -0 -0
37 C <5.42042,14.0755,26.9162> -0.00190436 -0.109367 0 -0 -0
38 C <6.62727,14.7569,27.0519> -0.0571441 -0.1599 0 -0 -0
39 C <7.55821,14.3433,28.003> -0.0518917 -0.162386 0.0297209 -0.0271385 -0
40 C <7.28086,13.2492,28.8245> -0.122789 -0.154636 0.00284687 -0.035069 -0
my question is, how is the scoring function calculated and which data does it use?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
There is also a num_tors_div term that reweights the energy based on the number of torsions like this: e / (1 + 0.05846*NTORSIONS)
Based on that, your molecule should have 13 rotatable bonds.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I'm trying to analyze the smina scoring function and I can't understand one thing.
For example for first conformation our affinity equals -7.404037
but sum of terms from per-atom interaction term values output doesn't equal to this affinity.
my question is, how is the scoring function calculated and which data does it use?
There is also a num_tors_div term that reweights the energy based on the number of torsions like this:
e / (1 + 0.05846*NTORSIONS)Based on that, your molecule should have 13 rotatable bonds.
Last edit: Maciej 2023-11-23