Autodock runs require the target structure in .pdbqt format (original PDB syntax, extended with partial charge and Autodock type information). such files can be prepared by the program AutoDockTools. This involves the following steps:

• Read the original PDB file
• Set default histidine protonation states (by default ADT protonates ALL histidines at both sites, resulting in a charged residue) via File->Preferences->Set defaults->Modify (older vesions may have just 'Set'). This will open a "Set User Preferences" widget; select the AutoDockTools tab and set the HIS protonation state as needed (usual default: ND1).
• Remove nonpolar hydrogens (if any) via Edit/Hydrogens
• Add polar hydrogens via Edit/Hydrogens
• Establish Autodock types via Edit/Atom
• Add partial charged via Edit/Charges/Gasteiger charges
• Save the final structure via File/Save/write PDBQT
• Establish the docking grid box center and grid size/numbers.
  This can be done via the Grid/Grid box menu - it brings up seven dials that can manipulate the size of the grid in the x/y/z directions by choosing the number of grids; the grid size (the default is 0.375 Å) and the position of the grid box center. Once the desired size and position is seen on the screen the center coordinates and the grid information have to be noted.

If the total charges added is not an integral number than it is most likely that some residues have missing or extra atoms. The program Simulaid can list all residuesr with non-integral charges - those have to be fixed manually.

There is a set of scripts and programs on Minerva that performs virtual screening with Autodock-4 and/or Autodock-Vina:

To use these tools, copy ALL files from /sc/hydra/projects/mezeim01b/fullscreen to the directory you plan to work. Copy your .pdbqt file (prepared by AutoDockTools) there. with Simulaid.

The script fullscreen.csh sets up the docking run interactively. When executed, it asks a number of questions. Formost among these are

• the software to use
• the target file name
• the ligand library specification (a directory of .mol2 or .pdbqt for Autodock 4 and Vina and a single file containing the ligands in .sdf or .mol2 format
• The docking grid specification (conveniently obtained using AutoDockTools)
• Number of processors to use
• For Autodock runs, the mode of running. One of the last question is
  "Do you want to only run the setup but skip docking for now"
  There are two options:
  • Ask the script to do the setup only (default answer). In this case the user can specify preparation for using the launcher facility at TACC or the selfsched script at MSSM. Chosing the MSSM option the script will prepare a file MACRO_grid/MACRO.dock or MACRO_vdock/MACRO.dock for Autodock-4 or Autodock-Vina, resp., (assuming that the target molecule is MACRO.pdbqt). This may take a while (ca 20,000 ligands per hour). Once the script is completed the selfsched.csh script needs to be updated: time limit (no more than 144 hours), number of nodes, and number of processors in the mpirun statement. Once done, the job has to be submitted as follows (substitute MACRO with your molecule's name):

    > cd MACRO_grid    (or > cd MACRO_vdock)
    > qsub -N MACRO ../selfsched.csh
    

    This will submit a single job using the number of processsor specified in the selfsched.csh script (via MPI).
  • Ask the script to run the screening. In that case the script will keep submitting serial (1-CPU) jobs, one for each ligand, but keeping the number of jobs in the que under the number of processors specified above.

Once the screening finished, the program Dockres can be used to sort, filter, analyze the docked ligand poses and extract PDB file(s) with the top-scoring ones.