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AutoDock Vina on Qarnot Cloud – documentation


by Tiphaine Bonniot - January 11, 2022 - Biotech

Introduction

AutoDock Vina is a free and open source simulation program for molecular modeling and in particular for docking. Molecular docking is a computer simulation of how a ligand might bind to a target. It is widely used for drug discovery and development. This article showcases with a simple example how to run a docking simulation with AutoDock Vina on Qarnot’s cloud computing platform.

Versions

The test case uses a AutoDock Vina version 1.1.2.

Release year Version
2011 1.1.2

If you are interested in another version, please send us an email at qlab@qarnot.com.

Prerequisites

Before launching the case, please ensure that the following prerequisites have been met.

Test case

This test case is a simple example of using AutoDock Vina on Qarnot cloud with the Python SDK. It showcases the docking of Indinavir, an HIV-1 protease inhibitor, used as an antiretroviral in the treatment of AIDS. The ligand, the target and the configuration file needed to launch the simulation can be downloaded from here. You need to unzip the indinavir-HIV-docking.zip archive to be able to launch the computation on Qarnot cloud.

Launching the case

Copy the following code in a Python script and save it in the same path as the indinavir-HIV-docking folder.

autodock.py

Be sure you have copied your authentication token in the script (instead of <<<MY_SECRET_TOKEN>>>) to be able to launch the task on Qarnot cloud.

Make sure that all input files (2 pdbqt file and 1 config.txt file) are in the same folder named indinavir-HIV-docking. Your working directory should look like this :

  • indinavir-HIV-docking/
    • config.txt : for readability, some command line options have been placed in a configuration file.
    • hsg1.pdbqt : crystal structure of human HIV.
    • ind.pdbqt : preprocessed Indinavir ligand.
  • autodock.py : Python script to run the computation on Qarnot cloud.

To launch this script, open a terminal in your working directory and execute python3 autodock.py &.

Results

At any given time, you can monitor the status of your task on the Console.

Successful AutoDock Vina execution on Qarnot’s cloud Console

You should now have an output folder in your working directory on your computer and a autodock-out bucket on Qarnot’s coud Console containing the output (results.pdbqt file, see bellow).

results.pdbqt
 

MODEL 1
REMARK VINA RESULT:     -17.1      0.000      0.000
REMARK   4 1HSG COMPLIES WITH FORMAT V. 2.0, 11-OCT-2000                        
ROOT
HETATM    1  N1  IND I 201       4.013   6.704  -3.128  1.00 28.25           N  
HETATM    2  C1  IND I 201       2.671   6.990  -3.702  1.00 30.30           C  
HETATM    3  C2  IND I 201       1.819   5.890  -4.302  1.00 27.27           C  
HETATM    4  C3  IND I 201       0.559   6.508  -4.846  1.00 28.85           C  
HETATM    5  O1  IND I 201       0.605   7.244  -5.824  1.00 29.59           O  
HETATM    6  N2  IND I 201      -0.565   6.231  -4.215  1.00 22.29           N  
HETATM    7  C4  IND I 201      -1.910   6.600  -4.519  1.00 23.47           C  
HETATM    8  C5  IND I 201      -2.771   6.188  -3.310  1.00 27.66           C  
HETATM    9  C6  IND I 201      -2.392   6.013  -5.677  1.00 21.71           C  
HETATM   10  C7  IND I 201      -2.109   8.048  -4.636  1.00 22.75           C  
HETATM   11  N3  IND I 201       2.725   5.354  -5.377  1.00 28.91           N  
HETATM   12  C8  IND I 201       4.172   5.201  -5.086  1.00 26.24           C  
HETATM   13  C9  IND I 201       4.812   6.217  -4.162  1.00 27.47           C  
HETATM   14  C10 IND I 201       2.268   4.201  -6.126  1.00 20.86           C  
HETATM   15  C11 IND I 201       2.348   4.367  -7.644  1.00 21.68           C  
HETATM   16  O2  IND I 201       2.352   2.999  -7.920  1.00 15.87           O  
HETATM   17  C12 IND I 201       1.250   5.022  -8.501  1.00 21.49           C  
HETATM   18  C13 IND I 201       1.427   5.175 -10.018  1.00 26.89           C  
HETATM   19  C14 IND I 201       0.212   5.841 -10.684  1.00 28.67           C  
HETATM   20  C15 IND I 201       0.383   5.998 -12.151  1.00 26.89           C  
HETATM   21  C16 IND I 201       0.713   4.931 -12.987  1.00 29.22           C  
HETATM   22  C17 IND I 201       0.899   5.130 -14.347  1.00 29.22           C  
HETATM   23  C18 IND I 201       0.751   6.419 -14.864  1.00 30.97           C  
HETATM   24  C19 IND I 201       0.412   7.491 -14.030  1.00 29.25           C  
HETATM   25  C20 IND I 201       0.227   7.274 -12.663  1.00 29.96           C  
HETATM   26  C21 IND I 201       2.680   5.968 -10.371  1.00 29.35           C  
HETATM   27  O3  IND I 201       2.921   7.048  -9.811  1.00 32.66           O  
HETATM   28  N4  IND I 201       3.397   5.482 -11.380  1.00 31.19           N  
HETATM   29  C22 IND I 201       4.413   6.280 -12.046  1.00 29.22           C  
HETATM   30  C23 IND I 201       4.492   5.977 -13.532  1.00 28.82           C  
HETATM   31  O4  IND I 201       4.202   4.608 -13.771  1.00 28.32           O  
HETATM   32  C24 IND I 201       5.886   6.390 -13.948  1.00 32.05           C  
HETATM   33  C25 IND I 201       6.856   6.205 -12.810  1.00 31.29           C  
HETATM   34  C26 IND I 201       8.216   6.074 -12.652  1.00 32.00           C  
HETATM   35  C27 IND I 201       8.717   5.873 -11.361  1.00 28.00           C  
HETATM   36  C28 IND I 201       7.855   5.808 -10.256  1.00 29.01           C  
HETATM   37  C29 IND I 201       6.478   5.927 -10.386  1.00 27.70           C  
HETATM   38  C30 IND I 201       5.889   6.120 -11.596  1.00 31.86           C  
HETATM   39  C31 IND I 201       4.634   7.756  -2.314  1.00 36.25           C  
HETATM   40  C32 IND I 201       3.998   8.231  -1.003  1.00 42.75           C  
HETATM   41  C33 IND I 201       4.053   7.492   0.187  1.00 47.41           C  
HETATM   42  N5  IND I 201       3.514   7.870   1.427  1.00 51.38           N  
HETATM   43  C34 IND I 201       2.893   9.115   1.337  1.00 50.60           C  
HETATM   44  C35 IND I 201       2.801   9.903   0.185  1.00 49.34           C  
HETATM   45  C36 IND I 201       3.364   9.455  -1.007  1.00 44.71           C  
HETATM   46  H1  IND I 201       2.824   7.705  -4.510  1.00  0.00           H  
HETATM   47  H2  IND I 201       2.070   7.406  -2.893  1.00  0.00           H  
HETATM   48  H3  IND I 201       1.584   5.170  -3.518  1.00  0.00           H  
HETATM   49  H4  IND I 201      -0.455   5.655  -3.368  1.00  0.00           H  
HETATM   50  H5  IND I 201      -3.812   6.452  -3.498  1.00  0.00           H  
HETATM   51  H6  IND I 201      -2.692   5.112  -3.157  1.00  0.00           H  
HETATM   52  H7  IND I 201      -2.421   6.709  -2.419  1.00  0.00           H  
HETATM   53  H8  IND I 201      -3.419   6.336  -5.848  1.00  0.00           H  
HETATM   54  H9  IND I 201      -1.772   6.312  -6.522  1.00  0.00           H  
HETATM   55  H10 IND I 201      -2.365   4.928  -5.574  1.00  0.00           H  
HETATM   56 1H1  IND I 201      -3.153   8.254  -4.867  1.00  0.00           H  
HETATM   57 2H1  IND I 201      -1.844   8.529  -3.694  1.00  0.00           H  
HETATM   58 3H1  IND I 201      -1.477   8.438  -5.433  1.00  0.00           H  
HETATM   59 4H1  IND I 201       4.705   5.266  -6.034  1.00  0.00           H  
HETATM   60 5H1  IND I 201       4.311   4.227  -4.617  1.00  0.00           H  
HETATM   61 6H1  IND I 201       5.680   5.735  -3.713  1.00  0.00           H  
HETATM   62 7H1  IND I 201       5.110   7.064  -4.780  1.00  0.00           H  
HETATM   63 8H1  IND I 201       1.226   4.015  -5.867  1.00  0.00           H  
HETATM   64 9H1  IND I 201       2.889   3.348  -5.854  1.00  0.00           H  
HETATM   65  H20 IND I 201       3.237   4.905  -7.969  1.00  0.00           H  
HETATM   66  H21 IND I 201       1.401   2.697  -8.174  1.00  0.00           H  
HETATM   67 2H2  IND I 201       1.119   6.037  -8.122  1.00  0.00           H  
HETATM   68 3H2  IND I 201       0.351   4.419  -8.374  1.00  0.00           H  
HETATM   69  H24 IND I 201       1.566   4.214 -10.516  1.00  0.00           H  
HETATM   70 5H2  IND I 201       0.017   6.839 -10.290  1.00  0.00           H  
HETATM   71 6H2  IND I 201      -0.706   5.271 -10.542  1.00  0.00           H  
HETATM   72  H27 IND I 201       0.826   3.931 -12.568  1.00  0.00           H  
HETATM   73  H28 IND I 201       1.155   4.296 -15.000  1.00  0.00           H  
HETATM   74  H29 IND I 201       0.901   6.592 -15.930  1.00  0.00           H  
HETATM   75  H30 IND I 201       0.292   8.492 -14.445  1.00  0.00           H  
HETATM   76  H31 IND I 201      -0.036   8.103 -12.007  1.00  0.00           H  
HETATM   77  H32 IND I 201       3.227   4.517 -11.699  1.00  0.00           H  
HETATM   78  H33 IND I 201       4.219   7.349 -11.952  1.00  0.00           H  
HETATM   79  H34 IND I 201       3.774   6.587 -14.081  1.00  0.00           H  
HETATM   80  H35 IND I 201       3.194   4.497 -13.957  1.00  0.00           H  
HETATM   81 6H3  IND I 201       5.902   7.439 -14.244  1.00  0.00           H  
HETATM   82 7H3  IND I 201       6.229   5.791 -14.791  1.00  0.00           H  
HETATM   83  H38 IND I 201       8.886   6.125 -13.510  1.00  0.00           H  
HETATM   84  H39 IND I 201       9.791   5.764 -11.212  1.00  0.00           H  
HETATM   85  H40 IND I 201       8.280   5.660  -9.263  1.00  0.00           H  
HETATM   86  H41 IND I 201       5.854   5.862  -9.495  1.00  0.00           H  
HETATM   87 2H4  IND I 201       4.687   8.644  -2.943  1.00  0.00           H  
HETATM   88 3H4  IND I 201       5.622   7.388  -2.034  1.00  0.00           H  
HETATM   89  H44 IND I 201       4.565   6.530   0.146  1.00  0.00           H  
HETATM   90  H45 IND I 201       2.438   9.510   2.245  1.00  0.00           H  
HETATM   91  H46 IND I 201       2.291  10.864   0.221  1.00  0.00           H  
HETATM   92  H47 IND I 201       3.304  10.054  -1.916  1.00  0.00           H  
ENDROOT
TORSDOF 5
ENDMDL

Wrapping up

That’s it! If you have any questions, please contact qlab@qarnot.com and we will help you with pleasure! You can read a more detailed article on this use case here : Molecular docking and cloud computing – Qarnot Blog or discover an other bio-technology use case on Qarnot here : Nucleotide sequence alignment with BlastN – Qarnot Blog or here: The journey of a protein in a glass of water – Qarnot Blog.

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