#Module 4 Molecular Docking Execution

Run the docking process in AutoDock Vina and obtain binding affinity results.

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Step 1 – Check Prepared Files

Ensure the following files are ready from Module 3:

• ACE_clean.pdbqt – Protein file (target)

• lisinopril.pdbqt – Ligand file (drug candidate)

• conf.txt – Docking configuration (grid box parameters)

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Step 2 – Create Docking Configuration File (conf.txt)

If not already done in Module 3, create a text file with:

receptor = ACE_clean.pdbqt
ligand = lisinopril.pdbqt

center_x = <value>
center_y = <value>
center_z = <value>

size_x = 20
size_y = 20
size_z = 20

exhaustiveness = 8
num_modes = 10

Replace <value> with the grid box coordinates obtained in Module 3.

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Step 3 – Run AutoDock Vina

1. Open Command Prompt / Terminal in the folder containing the files.

2. Run:

   bash
   
   vina --config conf.txt --out output.pdbqt --log log.txt
   

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Step 4 – Check Docking Results

• Open log.txt

• Look for:

  bash
  Affinity:  -9.2 kcal/mol
  

  Lower (more negative) = better binding.

• The top-ranked mode is usually the best pose.

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Step 5 – Convert Results for Visualization

• Convert output.pdbqt → .pdb using OpenBabel:

  bash
  
  obabel output.pdbqt -O output.pdb
  

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Step 6 – Visualize Binding

1. Open PyMOL or Chimera.

2. Load:

   • ACE_clean.pdb (protein)

   • output.pdb (docked ligand)

3. View ligand position in the binding site.

4. Highlight hydrogen bonds & interactions.

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Step 7 – Record Observations

• Binding energy values for each mode.

• Interaction residues.

• Potential drug-likeness observations