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AutoDockTools (ADT) for molecular docking research requires a specific scientific workflow and formal citation. This guide outlines how to structure a paper section based on the software's use. 1. Methods: Software & Installation Materials and Methods

section, specify the version and source of the software. AutoDockTools is part of the Software Details

: AutoDockTools (version 1.5.7) was used as the graphical user interface (GUI) to prepare the docking input files and analyze results. Availability : The software suite was downloaded from the official AutoDock Scripps Research website MGLTools download page 2. Experimental Protocol

A standard docking paper should detail these three phases of work performed in ADT: Receptor Preparation : The protein crystal structure (e.g., from the Protein Data Bank download autodock tools work

) was prepared by removing water molecules, adding polar hydrogens, and assigning Kollman charges . The final file was saved in Ligand Preparation

: Small molecule ligands were prepared by merging non-polar hydrogens, assigning Gasteiger charges , and defining rotatable bonds. These were also saved as Grid and Parameter Setup : The binding site was defined using a (dimension and coordinates specified) to generate the (Grid Parameter File) and (Docking Parameter File) for the simulation. 3. Required Citations

Scientific journals require you to cite the original developers of the software. Use the following primary references: AutoDock Vina 4) Installation — Windows

Publications. If you used AutoDock Vina in your work, please cite: J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli. ( AutoDock Vina

Citations — Autodock Vina 1.2.0 documentation - Read the Docs

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4) Installation — Windows

1. MGLTools/ADT:
   • Download Windows installer for MGLTools.
   • Run installer and follow prompts.
   • Launch "AutoDockTools" from Start Menu.
2. AutoDock Vina:
   • Download vina_xxx_win.zip, extract to folder (e.g., C:\Program Files\Vina).
   • Add folder to PATH: System Properties → Environment Variables → Path → New → paste folder.
   • Test: open Command Prompt, run vina --help.
3. OpenBabel:
   • Run installer; optionally add to PATH.

Method 1: Traditional Binary Installer (Windows only – may fail)

1. Go to the Scripps download page.
2. Download mgltools_win32_1.5.6_Setup.exe (yes, it’s 32-bit, but runs on 64-bit Windows).
3. Run the installer as Administrator.
4. Default path: C:\Program Files (x86)\MGLTools-1.5.6.
5. Launch ADT via Start Menu → MGLTools → AutoDock Tools.

If it doesn’t work: You’ll likely get an "MSVCR71.dll missing" or "Python 2.7 not found" error. Skip to Method 3. MGLTools/ADT:

9) Run AutoDock Vina

Command:

vina --config config.txt --out out.pdbqt --log log.txt

Or inline:

vina --receptor receptor.pdbqt --ligand ligand.pdbqt --center_x 0 --center_y 0 --center_z 0 --size_x 20 --size_y 20 --size_z 20 --out out.pdbqt --log log.txt

5.3 Preparing a PDBQT File (Ligand)

• Action: Loaded a ligand (e.g., inhibitor from same PDB or a small molecule SDF converted to PDB).
• Steps:
  1. Ligand → Input → Choose → selected ligand file.
  2. Ligand → Torsion Tree → Detect Root → auto-detected.
  3. Ligand → Output → Save as PDBQT → saved ligand.pdbqt.
• Result: File generated. Inspected text → contains partial charges and AutoDock atom types (e.g., C, OA, NA).