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I have docked 90,000 ligands and I have this unexpectedly very high positive affinity score. Other than that, if you look at the "ENERGY FROM SEARCH", it is a constant value throughout all the unexpected very high affinity score.
Here is the example
ENERGY FROM SEARCH: 340282346638528859811704183484516925440.0000
FINAL ENERGY:
Estimated Free Energy of Binding : 24700.086 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy : 31197.938 (kcal/mol)
Ligand - Receptor : 31197.938 (kcal/mol)
Ligand - Flex side chains : 0.000 (kcal/mol)
(2) Final Total Internal Energy : 1.936 (kcal/mol)
Ligand : 1.936 (kcal/mol)
Flex - Receptor : 0.000 (kcal/mol)
Flex - Flex side chains : 0.000 (kcal/mol)
(3) Torsional Free Energy : -6497.852 (kcal/mol)
(4) Unbound System's Energy : 1.936 (kcal/mol)
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 24700.0859 0.0000 0.0000
ENERGY FROM SEARCH: 340282346638528859811704183484516925440.0000
FINAL ENERGY:
Estimated Free Energy of Binding : 8311.212 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy : 9525.896 (kcal/mol)
Ligand - Receptor : 9525.896 (kcal/mol)
Ligand - Flex side chains : 0.000 (kcal/mol)
(2) Final Total Internal Energy : 1.443 (kcal/mol)
Ligand : 1.443 (kcal/mol)
Flex - Receptor : 0.000 (kcal/mol)
Flex - Flex side chains : 0.000 (kcal/mol)
(3) Torsional Free Energy : -1214.684 (kcal/mol)
(4) Unbound System's Energy : 1.443 (kcal/mol)
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 8311.2119 0.0000 0.0000
ENERGY FROM SEARCH: 340282346638528859811704183484516925440.0000
FINAL ENERGY:
Estimated Free Energy of Binding : 1381.443 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy : 1704.479 (kcal/mol)
Ligand - Receptor : 1704.479 (kcal/mol)
Ligand - Flex side chains : 0.000 (kcal/mol)
(2) Final Total Internal Energy : 2.270 (kcal/mol)
Ligand : 2.270 (kcal/mol)
Flex - Receptor : 0.000 (kcal/mol)
Flex - Flex side chains : 0.000 (kcal/mol)
(3) Torsional Free Energy : -323.037 (kcal/mol)
(4) Unbound System's Energy : 2.270 (kcal/mol)
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 1381.4429 0.0000 0.0000
I might be wrong here, but the structure and .pdbqt file for the highest scoring ligand looks fine.
Here is the .pdbqt for the highest scoring ligands:
REMARK Name = PV-008503443598
REMARK 6 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_2
REMARK 2 A between atoms: C_5 and C_7
REMARK 3 A between atoms: C_10 and C_11
REMARK 4 A between atoms: C_11 and O_12
REMARK 5 A between atoms: C_19 and C_21
REMARK 6 A between atoms: C_23 and C_24
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL 1 -0.822 -2.856 0.758 0.00 0.00 +0.000 C
ATOM 2 C UNL 1 -0.552 -1.354 0.825 0.00 0.00 +0.000 C
ATOM 3 C UNL 1 -1.464 -0.548 -0.121 0.00 0.00 +0.000 C
ATOM 4 N UNL 1 -1.249 0.912 0.031 0.00 0.00 +0.000 N
ATOM 5 C UNL 1 -2.162 1.849 -0.463 0.00 0.00 +0.000 C
ATOM 6 O UNL 1 -1.860 2.999 -0.769 0.00 0.00 +0.000 OA
ATOM 7 C UNL 1 0.157 1.350 0.070 0.00 0.00 +0.000 C
ATOM 8 C UNL 1 1.042 0.468 0.970 0.00 0.00 +0.000 C
ATOM 9 N UNL 1 0.852 -0.946 0.633 0.00 0.00 +0.000 N
ATOM 10 C UNL 1 1.586 -1.488 -0.425 0.00 0.00 +0.000 C
ATOM 11 O UNL 1 1.138 -2.289 -1.235 0.00 0.00 +0.000 OA
ENDROOT
BRANCH 5 12
ATOM 12 C UNL 1 -3.575 1.449 -0.618 0.00 0.00 +0.000 A
ATOM 13 C UNL 1 -4.160 1.497 -1.886 0.00 0.00 +0.000 A
ATOM 14 C UNL 1 -5.501 1.136 -2.043 0.00 0.00 +0.000 A
ATOM 15 C UNL 1 -6.265 0.732 -0.938 0.00 0.00 +0.000 A
ATOM 16 C UNL 1 -5.662 0.733 0.325 0.00 0.00 +0.000 A
ATOM 17 F UNL 1 -6.381 0.390 1.403 0.00 0.00 +0.000 F
ATOM 18 C UNL 1 -4.328 1.087 0.499 0.00 0.00 +0.000 A
BRANCH 15 19
ATOM 19 C UNL 1 -7.720 0.372 -1.057 0.00 0.00 +0.000 C
BRANCH 19 20
ATOM 20 O UNL 1 -8.038 -0.044 -2.380 0.00 0.00 +0.000 OA
ATOM 21 H UNL 1 -7.856 0.680 -2.999 0.00 0.00 +0.000 HD
ENDBRANCH 19 20
ENDBRANCH 15 19
ENDBRANCH 5 12
BRANCH 10 22
ATOM 22 C UNL 1 3.009 -1.065 -0.566 0.00 0.00 +0.000 C
ATOM 23 C UNL 1 4.060 -2.152 -0.586 0.00 0.00 +0.000 C
ATOM 24 C UNL 1 3.998 -1.198 0.580 0.00 0.00 +0.000 C
BRANCH 24 25
ATOM 25 C UNL 1 5.158 -0.245 0.769 0.00 0.00 +0.000 A
ATOM 26 C UNL 1 6.381 -0.720 1.274 0.00 0.00 +0.000 A
ATOM 27 C UNL 1 7.473 0.128 1.473 0.00 0.00 +0.000 A
ATOM 28 C UNL 1 7.364 1.481 1.173 0.00 0.00 +0.000 A
ATOM 29 C UNL 1 6.166 1.982 0.673 0.00 0.00 +0.000 A
ATOM 30 C UNL 1 5.077 1.126 0.476 0.00 0.00 +0.000 A
ENDBRANCH 24 25
ENDBRANCH 10 22
TORSDOF 5
I have attached files necessary to run a much faster and simpler unidock to reproduce the above error. It is worth noting that using these files also produced the constant "ENERGY FROM SEARCH", followed by high affinity scores.
The pdbqt file: rec_1CX2_clean.pdbqt
X coordinate: 24.644557093425625
Y coordinate: 21.8624152249135
Z coordinate: 16.1463062283737
docking size X: 20
docking size Y: 20
docking size Z: 20
exhaustiveness: 512
max step: 40
number of ligand modes: 1
Expected result
The text was updated successfully, but these errors were encountered:
I have docked 90,000 ligands and I have this unexpectedly very high positive affinity score. Other than that, if you look at the "ENERGY FROM SEARCH", it is a constant value throughout all the unexpected very high affinity score.
Here is the example
I might be wrong here, but the structure and .pdbqt file for the highest scoring ligand looks fine.
Here is the .pdbqt for the highest scoring ligands:
I have attached files necessary to run a much faster and simpler unidock to reproduce the above error. It is worth noting that using these files also produced the constant "ENERGY FROM SEARCH", followed by high affinity scores.
files_to_reproduce.zip
Settings used
Expected result
The text was updated successfully, but these errors were encountered: