Vina output is a pdbqt file, which is just like a regular PDB (with the addition of atom charge property), so the PyMol or whatever you use can display it. You can also strip the column, I think it's 11th, to make it a regular PDB. AutoDock has a very good FAQ and help pages, you should start looking there in the first place. →After converting pdb files into AutoDock input files (or.pdbqt files), you will see them under AutoDock tab as shown below (if you don’t see any files, right click and refresh under AutoDock tab) →Now the protein and ligand(s) files are ready for docking. →Click on Start Here button under Vina Wizard.
![Pdb to pdbqt autodock vina 2016 Pdb to pdbqt autodock vina 2016](/uploads/1/2/4/3/124325273/683480658.png)
Fitting a molecule and protein together
Overview
The fitting of a molecule into the active site of a protein is referred to as 'docking'. In our case, we may also 'dock' our molecule on the outside of the protein depending on the goals of our simulation.
To dock a molecule into a protein, the first step is to create the proper input files (.pdbqt) for the program. Then we are going to create a configuration file that we will use to run the docking algorithm. The algorithm will produce the nine best results according to some affinity score, and we will choose one and add it to our model.
Make the input files (.pdbqt)
We are going to use the scripts provided by Autodock to create the input files (.pdbqt) for the protein (.pdb) and ligand (.mol2). Run the following commands in the bash shell:
Note: The script will not assign charges for some atoms (e.g. Fe). You can edit the charges yourself in a text editor. The charge column is the second to last column on the line.
Make the configuration files (.conf)
Your configuration file is going to look something like this:
Run Autodock Vina
When the input and configuration files have been created, run the following command in the bash shell:
The input and configuration files must be saved in the current directory for the above command to find all the necessary files to run.
Final results
The output in the terminal will display the number of modes found (max nine) and order them according to an affinity score. You can open the results (output.pdbqt) in PyMOL and cycle through them using the movie buttons. Also open the original protein (protein.pdb) to see how the molecule fits into the protein.
If you don't find a conformation you want, you can change the size or location of the search box in the configuration file and run Vina again. Once you find the conformation you want, save the conformation in PyMOL as a .pdb. Then copy the lines from this .pdb into your original protein.pdb. Save this file.
More Information
The Autodock scripts can be found at http://autodock.scripps.edu/faqs-help/faq/where-can-i-find-the-python-scripts-for-preparing-and-analysing-autodock-dockings/?searchterm=prepare_ligand. Click on each script to learn more about the options available.
Autodock Vina can be found at http://vina.scripps.edu/
For more information on the format of .pdbqt, check out http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
For this tutorial we are talking about small molecules (e.g. the size of caffeine). Bigger molecules, and especially those with many rotatable bonds (>32), will take longer to dock in Autodock Vina.
Thanks for visiting. -Ylok