Jcatazaro: Created page with "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" # Ope..."

2017-03-14T21:23:00Z

Created page with "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" # Ope..."

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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

Setting Up a Virtual Screen with AutoDock - Revision history

Jcatazaro: Created page with "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" # Ope..."