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I am experiencing some unexpected behaviour with the Vina scoring function, in particular the hydrophobic interaction term. From what I understand the score is calculated as the following sum: $$c=\sum_{i < j} f_{t_i t_j}(r_{ij})$$
And the hydrophobic term is always non-negative (but then weighted to become negative). For this reason I expect that adding atoms should always increase (or leave unchanged) the hydrophobic interaction term. However this is not what I observe. With the following example I find the interaction term for a molecule to be 1.452 while the interaction term for a subset of atoms is 1.766. Note that I extract the subset by deleting lines in the pdbqt file so the atom types don't change (although the molecule becomes unrealistic). I thought I could be observing some difference due to intra-molecule interactions but from what I understand these aren't included in the lig_inter part of the score output.
Could it be to do with how I've built my toy example with unrealistic molecules and proteins? Or have I fundamentally misunderstood some aspect of how the scoring function is built?
I would much appreciate any help to see what I am missing.
ATOM 39 CZ TYR A 7 0.217 -5.062 13.014 1.00 0.00 0.131 A
ATOM 40 OH TYR A 7 -0.670 -4.109 13.459 1.00 0.00 -0.190 OA
ATOM 750 ND1 HIS A 96 -4.805 -4.973 14.161 1.00 0.00 -0.227 NA
ATOM 752 CE1 HIS A 96 -4.859 -3.698 14.442 1.00 0.00 0.199 A
ATOM 1550 CG2 THR A 199 -1.424 -1.061 14.615 1.00 0.00 0.038 C
ATOM 1898 O ASN A 243 -2.883 -6.788 13.243 1.00 0.00 -0.268 OA
mol.pdbqt
REMARK Name =
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 S UNL 1 -6.312 3.596 15.766 0.00 0.00 +0.000 S
ATOM 2 C UNL 1 -5.391 2.199 16.010 0.00 0.00 +0.000 A
ATOM 3 C UNL 1 -4.122 2.251 15.429 0.00 0.00 +0.000 A
ATOM 4 C UNL 1 -3.943 3.498 14.755 0.00 0.00 +0.000 A
ATOM 5 C UNL 1 -2.720 3.866 13.998 0.00 0.00 +0.000 C
ATOM 6 C UNL 1 -2.676 5.387 13.749 0.00 0.00 +0.000 C
ATOM 7 C UNL 1 -3.910 5.973 13.106 0.00 0.00 +0.000 C
ATOM 8 S UNL 1 -5.172 5.969 14.361 0.00 0.00 +0.000 S
ATOM 9 C UNL 1 -5.089 4.322 14.860 0.00 0.00 +0.000 A
ATOM 10 C UNL 1 -3.617 7.415 12.654 0.00 0.00 +0.000 C
ATOM 11 O UNL 1 -6.440 6.188 13.719 0.00 0.00 +0.000 OA
ATOM 12 O UNL 1 -4.808 6.760 15.507 0.00 0.00 +0.000 OA
ENDROOT
BRANCH 2 13
ATOM 13 S UNL 1 -6.025 0.889 16.944 0.00 0.00 +0.000 S
ATOM 14 O UNL 1 -7.450 0.942 16.779 0.00 0.00 +0.000 OA
ATOM 15 O UNL 1 -5.492 0.980 18.275 0.00 0.00 +0.000 OA
ATOM 16 N UNL 1 -5.472 -0.571 16.240 0.00 0.00 +0.000 NA
ENDBRANCH 2 13
BRANCH 5 17
ATOM 17 N UNL 1 -2.741 3.129 12.722 0.00 0.00 +0.000 NA
BRANCH 17 18
ATOM 18 C UNL 1 -1.473 3.172 11.982 0.00 0.00 +0.000 C
ATOM 19 C UNL 1 -1.554 2.103 10.891 0.00 0.00 +0.000 C
ENDBRANCH 17 18
ENDBRANCH 5 17
TORSDOF 0
subset_of_mol.pdbqt made up of atoms 4, 5, 18, and 19 of the molecule above.
REMARK Name =
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL 1 -4.122 2.251 15.429 0.00 0.00 +0.000 A
ATOM 2 C UNL 1 -3.943 3.498 14.755 0.00 0.00 +0.000 A
ATOM 3 C UNL 1 -1.473 3.172 11.982 0.00 0.00 +0.000 C
ATOM 4 C UNL 1 -1.554 2.103 10.891 0.00 0.00 +0.000 C
ENDROOT
TORSDOF 0
The text was updated successfully, but these errors were encountered:
Vina uses its own types internally, and carbons that are bound to some heteroatoms are not considered hydrophobic. So, the system with four atoms has four hydrophobic carbons, but in the original molecule atom 18 (atom 3 in the four-atom system) is not hydrophobic because it is bonded to nitrogen.
I am experiencing some unexpected behaviour with the Vina scoring function, in particular the hydrophobic interaction term. From what I understand the score is calculated as the following sum:
$$c=\sum_{i < j} f_{t_i t_j}(r_{ij})$$
And the hydrophobic term is always non-negative (but then weighted to become negative). For this reason I expect that adding atoms should always increase (or leave unchanged) the hydrophobic interaction term. However this is not what I observe. With the following example I find the interaction term for a molecule to be
1.452
while the interaction term for a subset of atoms is1.766
. Note that I extract the subset by deleting lines in the pdbqt file so the atom types don't change (although the molecule becomes unrealistic). I thought I could be observing some difference due to intra-molecule interactions but from what I understand these aren't included in thelig_inter
part of the score output.Could it be to do with how I've built my toy example with unrealistic molecules and proteins? Or have I fundamentally misunderstood some aspect of how the scoring function is built?
I would much appreciate any help to see what I am missing.
Code to reproduce
protein_fragment.pdbqt
mol.pdbqt
subset_of_mol.pdbqt made up of atoms 4, 5, 18, and 19 of the molecule above.
The text was updated successfully, but these errors were encountered: