Contribution

Please make use of our small tutorial/protocol on using Autodock Vina (also found in Experiments Page)

AutoDock Vina Protocol

Developed by iGEM Team and Mehmet Emre Erkanli

  • Open the protein and ligand in Pymol one at a time - clean up (delete unnecessary chains for protein) and save as pdb
  • Open Autodock → Read Molecule → open protein/enzyme (ferritin in our case)
    • Edit → delete water molecules
    • Edit Hydrogen → selection options: polar, non-bond order, yes
    • Edit Charges → add Kollman charge
    • Save edited protein as a macromolecule (pdbqt)
  • Open the peptide.pdb as a ligand input and save it as peptide.pdbqt (ligand output)
  • Open the gridbox → adjust spacing to 1.0 → adjust box dimensions until it covers the entire protein (macromolecule) → output grid file as grid.txt
  • Create text file “config.txt” and add which files will be receptor (protein) and ligand (peptide), dimensions (size, center coordinates) of the gridbox from grid.txt, and the energy range and exhaustiveness of the program
  • Run Autodock vina - select file names vina and config.txt for two inputs → run program
  • Command screen should pop up showing progress → will get a table of binding affinities and rmsd’s of the different ligand conformations
  • Can save output file as a pdb and open to view ligand conformations with the macromolecule in Pymol and/or Autodock Vina

Here is the first config.txt we made (ligand that was only energy minimized in Chemdraw + Heavy Chain Ferritin)

conf.txt

Here are the results we got on the command screen

cmd

Here is the first ligand conformation with ferritin

autodock