View source for Setting Up a Virtual Screen with AutoDock

Setting Up a Virtual Screen with AutoDock


#	Install MGLTools and AutoDock, download raccoon.py
#	Navigate to the MGLTools directory
## "cd /Library/MGLTools/1.5.6/bin"
#	Open raccoon.py with pythonsh in the MGLTools directory
## "./pythonsh ~/Downloads/raccoon.py"
#	Add your pdb file
#	Add the directory with the ligand structure files (mol2 or pdbqt format)
##The mol2 files will be converted to pdbqt at this point.
#	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. 
#	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.
#	Set output directory
#	All the scripts and files necessary will be created. Execute the following in your terminal:
## "./RunVS.sh"
#	Alternatively, edit and use RunVS.py to use multiprocessing on your computer.
#	 In the resulting .dlg file, the ligand with the lowest energy is the “best” binder.
#	 summary.py can be used to quickly sort the ligands if RunVS.py was used.
#	Open AutoDock, import the .dlg and open the protein pdb(qt)
#	Export the docked complex to a single pdbqt
#	The pdbqt can be opened in Chimera as a pdb