PS C:\Users\User\Desktop\docking_test> $vina = "C:\Users\User\AppData\Local\Programs\Vina\vina_1.2.7_win.exe" PS C:\Users\User\Desktop\docking_test> $receptors = @("OCT4_v3","SOX2_v3","KLF4_v3") PS C:\Users\User\Desktop\docking_test> $ligands = @("O4I4_v2","Resveratrol_v2","NMN_v2","Azacitidine_v2","VPA_v2") PS C:\Users\User\Desktop\docking_test> PS C:\Users\User\Desktop\docking_test> foreach($r in $receptors) { >> foreach($l in $ligands) { >> $out = "results_${r}_${l}.pdbqt" >> Write-Host "Running $r + $l..." >> & $vina --receptor "pdb\$r.pdbqt" --ligand "docking_ready\ligands\$l.pdbqt" --center_x 0 --center_y 0 --center_z 0 --size_x 30 --size_y 30 --size_z 30 --exhaustiveness 8 --num_modes 10 --out $out >> } >> } Running OCT4_v3 + O4I4_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\OCT4_v3.pdbqt Ligand: docking_ready\ligands\O4I4_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -1747925323) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -5.579 0 0 2 -5.391 2.15 4.251 3 -5.148 23.12 23.8 4 -5.103 23.96 25.03 5 -5.058 22.49 23.52 6 -4.948 22.49 23.7 7 -4.897 14.64 15.82 8 -4.862 14.84 15.93 9 -4.816 22.88 23.91 10 -4.651 23.54 24.75 Running OCT4_v3 + Resveratrol_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\OCT4_v3.pdbqt Ligand: docking_ready\ligands\Resveratrol_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 384737164) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -6.017 0 0 2 -6.002 0.4517 7.306 3 -5.973 10.31 13.06 4 -5.947 7.149 11.19 5 -5.716 9.933 11.47 6 -5.481 1.346 2.08 7 -5.475 6.6 9.483 8 -5.44 1.071 2.314 9 -5.362 23.47 25.08 10 -5.319 6.559 9.398 Running OCT4_v3 + NMN_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\OCT4_v3.pdbqt Ligand: docking_ready\ligands\NMN_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -1502730380) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -4.502 0 0 2 -4.481 2.239 3.382 3 -4.293 17.16 19.28 4 -4.239 2.647 5.323 5 -4.154 2.668 4.735 6 -4.13 22.51 23.84 7 -3.965 2.597 3.815 8 -3.937 22.97 24.04 9 -3.928 3.616 5.448 10 -3.908 4.471 6.274 Running OCT4_v3 + Azacitidine_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\OCT4_v3.pdbqt Ligand: docking_ready\ligands\Azacitidine_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 1330059256) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -5.146 0 0 2 -5.094 2.358 6.413 3 -5.021 14.73 17.89 4 -4.997 1.559 2.812 5 -4.893 2.616 3.753 6 -4.846 2.268 7.099 7 -4.757 14.85 17.69 8 -4.692 14.35 16.55 9 -4.463 14.44 17.62 10 -4.42 3.022 5.888 Running OCT4_v3 + VPA_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\OCT4_v3.pdbqt Ligand: docking_ready\ligands\VPA_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -1921406376) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -3.74 0 0 2 -3.698 2.315 3.533 3 -3.666 2.148 3.498 4 -3.571 23.56 24.69 5 -3.554 1.917 3.432 6 -3.469 22.65 23.71 7 -3.461 0.9647 3.155 8 -3.425 22.66 23.61 9 -3.313 1.563 3.133 10 -3.298 24.3 26.12 Running SOX2_v3 + O4I4_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\SOX2_v3.pdbqt Ligand: docking_ready\ligands\O4I4_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -156660935) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -5.54 0 0 2 -5.01 14.48 16.01 3 -5.005 14.21 15.65 4 -5.004 2.396 5.103 5 -4.967 14.56 16.17 6 -4.94 11.73 13.82 7 -4.917 2.183 4.349 8 -4.902 10.96 12.15 9 -4.85 2.499 4.815 10 -4.668 14.56 15.82 Running SOX2_v3 + Resveratrol_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\SOX2_v3.pdbqt Ligand: docking_ready\ligands\Resveratrol_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 92676234) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -6.364 0 0 2 -6.064 14.44 17.02 3 -5.953 19.25 21.65 4 -5.926 2.157 7.838 5 -5.921 2.203 3.624 6 -5.888 14.5 17.1 7 -5.836 0.6294 7.217 8 -5.833 1.629 7.683 9 -5.763 13.07 15.43 10 -5.747 5.717 8.817 Running SOX2_v3 + NMN_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\SOX2_v3.pdbqt Ligand: docking_ready\ligands\NMN_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -69861879) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -4.514 0 0 2 -4.414 14.09 15.74 3 -4.337 2.473 5.392 4 -4.296 13.7 15.01 5 -4.225 11.15 12.43 6 -4.036 21.53 22.95 7 -4.025 14.06 15.41 8 -3.976 2.745 4.214 9 -3.958 21.71 23.8 10 -3.908 14.32 15.73 Running SOX2_v3 + Azacitidine_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\SOX2_v3.pdbqt Ligand: docking_ready\ligands\Azacitidine_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -480079536) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -4.942 0 0 2 -4.888 3.976 6.82 3 -4.888 3.71 6.354 4 -4.782 12.49 14.44 5 -4.767 2.78 6.14 6 -4.762 12.4 14.03 7 -4.749 12.79 13.84 8 -4.611 12.79 14.23 9 -4.547 12.5 14.25 10 -4.512 3.303 3.904 Running SOX2_v3 + VPA_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\SOX2_v3.pdbqt Ligand: docking_ready\ligands\VPA_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 837431754) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -3.579 0 0 2 -3.472 23.16 24.38 3 -3.441 10.18 11.29 4 -3.44 23.41 24.47 5 -3.405 22.88 24.3 6 -3.371 9.695 10.85 7 -3.349 0.9271 3.107 8 -3.264 9.923 11.02 9 -3.231 1.974 3.848 10 45.22 15.3 16.68 Running KLF4_v3 + O4I4_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\KLF4_v3.pdbqt Ligand: docking_ready\ligands\O4I4_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 1924074198) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -6.024 0 0 2 -5.979 2.212 3.885 3 -5.732 8.173 10.58 4 -5.709 2.241 3.685 5 -5.528 5.526 7.533 6 -5.487 3.943 5.696 7 -5.383 2.013 4.538 8 -5.328 3.254 6.291 9 -5.315 4.576 7.795 10 -5.249 6.292 9.451 Running KLF4_v3 + Resveratrol_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\KLF4_v3.pdbqt Ligand: docking_ready\ligands\Resveratrol_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -1918026395) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -6.203 0 0 2 -6.077 8.163 10.72 3 -6.07 7.764 8.455 4 -6.013 0.4563 7.414 5 -5.899 14.99 16.89 6 -5.89 6.139 7.386 7 -5.79 7.567 8.936 8 -5.65 7.071 7.935 9 -5.521 5.917 7.058 10 -5.433 16.49 17.52 Running KLF4_v3 + NMN_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\KLF4_v3.pdbqt Ligand: docking_ready\ligands\NMN_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 409744025) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -4.98 0 0 2 -4.911 5.769 7.779 3 -4.861 2.722 4.698 4 -4.779 4.133 5.766 5 -4.762 5.97 7.483 6 -4.711 2.911 4.686 7 -4.664 10.49 11.97 8 -4.659 3.397 4.809 9 -4.642 3.018 5.19 10 -4.601 2.809 4.29 Running KLF4_v3 + Azacitidine_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\KLF4_v3.pdbqt Ligand: docking_ready\ligands\Azacitidine_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: -1252924451) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -5.791 0 0 2 -5.717 1.891 6.192 3 -5.647 2.895 4.566 4 -5.644 2.118 6.219 5 -5.583 4.156 6.322 6 -5.497 2.728 4.29 7 -5.415 2.01 6.198 8 -5.406 2.905 4.181 9 -5.397 3.028 6.021 10 -5.302 2.789 6.257 Running KLF4_v3 + VPA_v2... AutoDock Vina v1.2.7 ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli # # AutoDock Vina 1.2.0: New Docking Methods, Expanded Force # # Field, and Python Bindings, J. Chem. Inf. Model. (2021) # # DOI 10.1021/acs.jcim.1c00203 # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, J. Comp. Chem. (2010) # # DOI 10.1002/jcc.21334 # # # # Please see https://github.com/ccsb-scripps/AutoDock-Vina for # # more information. # ################################################################# Scoring function : vina Rigid receptor: pdb\KLF4_v3.pdbqt Ligand: docking_ready\ligands\VPA_v2.pdbqt Grid center: X 0 Y 0 Z 0 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1 Computing Vina grid ... done. WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs. Performing docking (random seed: 1671054632) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| *************************************************** mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -3.651 0 0 2 -3.645 2.274 3.57 3 -3.527 8.895 10.53 4 -3.51 2.628 4.067 5 -3.5 11.9 12.97 6 -3.481 2.496 3.669 7 -3.46 8.92 10.38 8 -3.456 1.743 3.577 9 -3.415 2.69 3.871 10 -3.386 2 3.933 PS C:\Users\User\Desktop\docking_test> Write-Host "All done!" All done! PS C:\Users\User\Desktop\docking_test>