Molecular Docking Setup with AutoDock Vina

Directory Structure

• input/
  • ligands/ (PDB, MOL2, SDF formats)
  • receptor/
• output/
  • poses/
  • scores/
  • analysis/
• config/
• scripts/
• logs/

Usage

1. Place receptor PDB file in input/receptor/
2. Place ligand files in appropriate input/ligands/ subdirectory
3. Run preparation scripts:
   • ./scripts/prep_receptor.sh <receptor.pdb>
   • ./scripts/prep_ligands.sh <ligand_directory>
4. Run docking:
   • ./scripts/dock.sh <receptor.pdbqt> <ligand.pdbqt>
5. Analyze results:
   • ./scripts/analyze_results.sh

Requirements

• AutoDock Vina
• MGLTools (for preparation scripts)