Setting Up a Virtual Screen with AutoDock

Setting Up a Virtual Screen with AutoDock

1. Install MGLTools and AutoDock, download raccoon.py
2. Navigate to the MGLTools directory
   1. "cd /Library/MGLTools/1.5.6/bin"
3. Open raccoon.py with pythonsh in the MGLTools directory
   1. "./pythonsh ~/Downloads/raccoon.py"
4. Add your pdb file
5. Add the directory with the ligand structure files (mol2 or pdbqt format)
   1. The mol2 files will be converted to pdbqt at this point.
6. Keep all default parameters for a general screen. For a more robust screen on a small set of ligands change the number of genetic algorithm iterations to be greater than 10.
7. Add your grid parameter file. This can be generated by opening the AutoDockTools graphical interface and creating a box around your binding site entire protein.
8. Set output directory
9. All the scripts and files necessary will be created. Execute the following in your terminal:
   1. "./RunVS.sh"
10. Alternatively, edit and use RunVS.py to use multiprocessing on your computer.
11. In the resulting .dlg file, the ligand with the lowest energy is the “best” binder.
12. summary.py can be used to quickly sort the ligands if RunVS.py was used.
13. Open AutoDock, import the .dlg and open the protein pdb(qt)
14. Export the docked complex to a single pdbqt
15. The pdbqt can be opened in Chimera as a pdb