Instructions for running Autodock-4 and/or Autodock-Vina on Minerva

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:

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

If Autodock-4 is selected, the script will offer to submit Autodock-Vina as well.

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.

Last modified: 06/05/2020