PyAutodock/cAutodock

Autodock scoring function can be used in ePMV to do interactive docking. As PyAutoDock is present by default but lack of performance to let real-time computation we encourage you to get the cAutodock package :

- Linux : use our cvs repository. Open a terminal window or Windows shell, navigate to your $MGLTOOLS/MGLToolsPckgs directory (see Installation, then follow these command-line instructions:

cvs -d:pserver:anonymous@mgl1.scripps.edu:/opt/cvs co cAutoDockDIST

cd cAutoDockDIST

../../bin/pythonsh setup.py build

../../bin/pythonsh setup.py install --install-platlib=$MGLTOOLS/MGLToolsPckgs

cd ..

cvs -d:pserver:anonymous@mgl1.scripps.edu:/opt/cvs co memoryobjectDIST

cd memoryobjectDIST

../../bin/pythonsh setup.py build

../../bin/pythonsh setup.py install --install-platlib=$MGLTOOLS/MGLToolsPckgs

- Windows : Theses two modules are part of the actual mgltoosl distribution we provide for Windows.

- Mac : download the following zip archive and extract the two modules in your MGLToolsPckgs. cAD.zip

In order to perform an interactive docking using the AutoDock scoring, you need two molecules one receptor and one ligand molecule in the pdbqt format specific to AutoDock. You need to display the CPK at least once for both molecule, as most of the synchronization use the CPK sphere positions. Then you can open the PyAutoDock dialog and setup the computation.

In the Recpetor and Ligand entry field you need to specify which atoms will be used for both molecule during the computation using the PMV syntax (Molecule:Chain:Residues:Atoms, hsg1:::; represent all atoms of all residues of all chains of the molecule called hsg1). You need also to specify the type of score you want to use:

• • python based : PyPairWise, ad3Score and ad4Score

  • c based : c_ad3Score and PairWise

Once you have add a scorer, you can :

• • display Label for the computed score

  • activate the real time computation which require that you activate the real-time synchronization in the ePMV option (Edit->options->synchro realtime) if its not already done. now the score should reflect the ligand position regarding the receptor.

  • Color Rec : for every score computation the CPK representation of the receptor will be colored according the score at the atoms levels (don't check if you are in real-time and the receptor is a big protein)

  • Color Lig : for every score computation the CPK representation of theligand will be colored according the score at the atoms levels

  • Store: if check you should be able to store the conformation in the data player (NOT IMPLEMENTED YET). In order to save your docking pose, you can instead apply the transformation to the molecule and then save it to a PDB file. Go to Edit->Apply Transformation, which will apply the current cpk/sphere position to the molecule, and then save the molecule as PDB.

There are demo files in MGLToolsPckgs/ePMV/demo: hsg1.pdbqt and ind.pdbqt.

• • Browse to load both pdbqt file

  • Display the Atoms and the Lines for both molecules

  • Open the PyAutoDock extension

  • Select c_ad3Score as the type of score

  • Click on 'Add Scorer'

  • Verify that the scorer is available and select it in the Available scorer pull-down menu

  • Check Display Label : this will create the label object for the score

  • Check Color Lig

  • Click on Get Score

  • Change the position of the obj "ind" (top hierarchy of the ligand molecule)

  • Click on Get Score

  • If nothing happens, and the score stays at 1000.0 and the ligand is red, that's means that you need to synchronize ePMV and your host:

    • in ePMV dialog go to Edit->Option

    • Check Synchro realtime

    • Click OK

  • Click on Get Score: You should see now the score of your actual complex rec-lig

  • Check Real time, and start manipulating the "ind" top hierarchy object, you should see the score evolved as you move the ligand

Once the scoring is set-up you can start using the physics capability of your host for handling collision (vdw repulsion) as well as flexibility.