Docking error code

[emilytheis1]

I'm using a known molecule, converted to pdbqt using MGTools, and a known protein, also convered to pdbqt using MGTools 1.5.7. I added hydrogens and charges using MGTools. I defined my area of interest using center and size coordinates, and checked it using the visualization part of MGTools. However, I'm still getting Error 1 when I try to run autodock vina, without any further description. What could be going wrong, or what else could I do to debug?? I'm running AutoDock Vina 1.2.3. This is the command I'm using: vina_cmd = [ "vina", "--receptor", receptor_path, "--ligand", ligand_path, "--center_x", str(center_x), "--center_y", str(center_y), "--center_z", str(center_z), "--size_x", str(size_x), "--size_y", str(size_y), "--size_z", str(size_z), "--exhaustiveness", "20", "--num_modes", "9",
"--energy_range", "3", "--out", output_path ]

[rwxayheee]

Hello @emilytheis1 Please use the latest version. You could get it from: https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.5 It seems like there's a problem with molecule.pdbqt. Could you please share the file?

[emilytheis1]

When I import autodock using the command !apt-get install -y vina , it automatically chooses 1.2.3. Is there a way to specify 1.2.5?

This is my molecule.pdqt file attached, changed to .txt for upload molecule.txt

[rwxayheee]

Hi @emilytheis1, This might not be a valid pdbqt for ligand. For ligand, Vina expects keywords that describe the molecule's flexibility such as ROOT and BRANCH See an example ligand pdbqt as follows:

REMARK SMILES NC(N)=[NH+]CCC[C@H]([NH3+])C(=O)[O-]
REMARK SMILES IDX 6 1 5 2 4 3 2 5 1 6 3 7 7 12 8 13 9 14 10 18 11 19 12 20
REMARK H PARENT 4 4 1 8 1 9 3 10 3 11 9 15 9 16 9 17
ROOT
ATOM      1  C   UNL     1      -0.235  -0.395   0.100  1.00  0.00     0.044 C 
ENDROOT
BRANCH   1   2
ATOM      2  C   UNL     1       0.990   0.508  -0.083  1.00  0.00     0.197 C 
BRANCH   2   3
ATOM      3  N   UNL     1       2.178  -0.282  -0.422  1.00  0.00    -0.278 N 
ATOM      4  H   UNL     1       2.076  -1.321  -0.499  1.00  0.00     0.260 HD
BRANCH   3   5
ATOM      5  C   UNL     1       3.358   0.238  -0.633  1.00  0.00     0.338 C 
ATOM      6  N   UNL     1       3.585   1.653  -0.547  1.00  0.00    -0.291 N 
ATOM      7  N   UNL     1       4.459  -0.617  -0.960  1.00  0.00    -0.291 N 
ATOM      8  H   UNL     1       2.830   2.333  -0.314  1.00  0.00     0.256 HD
ATOM      9  H   UNL     1       4.540   2.037  -0.722  1.00  0.00     0.256 HD
ATOM     10  H   UNL     1       4.336  -1.651  -1.032  1.00  0.00     0.256 HD
ATOM     11  H   UNL     1       5.407  -0.215  -1.131  1.00  0.00     0.256 HD
ENDBRANCH   3   5
ENDBRANCH   2   3
ENDBRANCH   1   2
BRANCH   1  12
ATOM     12  C   UNL     1      -1.485   0.431   0.440  1.00  0.00     0.075 C 
BRANCH  12  13
ATOM     13  C   UNL     1      -2.706  -0.452   0.783  1.00  0.00     0.227 C 
BRANCH  13  14
ATOM     14  N   UNL     1      -3.171  -1.216  -0.384  1.00  0.00    -0.350 N 
ATOM     15  H   UNL     1      -2.470  -1.947  -0.638  1.00  0.00     0.345 HD
ATOM     16  H   UNL     1      -4.067  -1.707  -0.154  1.00  0.00     0.345 HD
ATOM     17  H   UNL     1      -3.329  -0.585  -1.203  1.00  0.00     0.345 HD
ENDBRANCH  13  14
BRANCH  13  18
ATOM     18  C   UNL     1      -3.820   0.410   1.316  1.00  0.00     0.099 C 
ATOM     19  O   UNL     1      -4.413   1.226   0.562  1.00  0.00    -0.544 OA
ATOM     20  O   UNL     1      -4.185   0.323   2.654  1.00  0.00    -0.544 OA
ENDBRANCH  13  18
ENDBRANCH  12  13
ENDBRANCH   1  12
TORSDOF 7

apt-get doesn't seem to have the most up-to-date version of vina. If you're using Google Colab you can simply download the executable and upload to a convenient location in your drive

[emilytheis1]

So I made the pdbqt files using MGLTools... is that outdated? I've also tried making the pdbqt files using Open Babel (attached) but that resulted in an error code of 1 as well.

I'll give the executable a try too, where do I find it?

molecule_1.txt

[rwxayheee]

Hi @emilytheis1 It seems like you're preparing ethanol as the ligand. It should be ok to run docking calculations with the OpenBabel pdbqt file. The most recently developed project we have here for ligand and receptor preparation is Meeko, a Python package. With Meeko, you can prepare ligand in command line or Python.

The project's Git repository is: https://github.com/forlilab/Meeko/

We have very recently released a new version and put up the documentation. Here you can find some basic usage on ligand preparation. https://meeko.readthedocs.io/en/release/lig_prep_basic.html

Please give it a try, and in case you're interested in integration with Google Colab notebooks, I have made some sample sessions that are full docking calculations from preparation to pose export. See a collection also from Meeko documentation: https://meeko.readthedocs.io/en/release/colab_examples.html

[rwxayheee]

You could find executables for the latest version of Vina from the Release page of this repository: https://github.com/ccsb-scripps/AutoDock-Vina/releases Thanks for letting us know the apt-get version issue!

[emilytheis1]

Those Meeko examples are so helpful, thank you! got autodoc vina running using those.