Tag
AutoDock Vina
Molecular Modeling How to Remove Water Molecules From a PDB File for Docking Strip HOH waters and crystallisation additives from a PDB file with PyMOL, ChimeraX or pdb-tools, and learn which structural waters to keep. Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Dock a Ligand to a GPCR or Membrane Protein with AutoDock Vina (Step by Step) Dock a ligand into a GPCR with AutoDock Vina: pick the right activation state, strip BRIL and T4 lysozyme, and place the… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling AutoDock Vina Errors and How to Fix Them: The 10 That Stop Beginners Decode the 10 AutoDock Vina errors that stop beginners, from PDBQT parsing failures to grid box mistakes, with the exact command that… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Discovery Studio Visualizer Tutorial: How to Analyse Docking Results and Make 2D Interaction Diagrams Load your docked pose, list every contact with its distance, and export the 2D interaction diagram your thesis needs. Follow the full… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Do Ensemble Docking with MD Snapshots (Receptor Flexibility Beyond Flexible Side Chains) Learn ensemble docking step by step: run MD on the apo protein, cluster the trajectory, dock into every snapshot, then combine the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Handle Metal Ions in Molecular Docking and MD (Zinc, Magnesium and Iron, Step by Step) Stop deleting the zinc. Learn when to keep a metal ion, how to dock into a metalloprotein with AutoDock4Zn, and how to… Dr. Abdul Rajjak Shaikh 15 min read Drug Design Why AutoDock Vina Gives Different Results Every Time (Exhaustiveness, Seed and Reproducible Docking) Vina's search is non-deterministic, so scores shift between runs. Learn what exhaustiveness controls, how --seed fixes it, and how to report both. Dr. Abdul Rajjak Shaikh 11 min read Molecular Modeling How to Install AutoDock Vina on Windows 10 and 11: A Step-by-Step Guide for Beginners (Vina 1.2.7 + AutoDockTools) Install AutoDock Vina 1.2.7 on Windows the way it ships today: one bare .exe, no MSI, plus MGLTools for AutoDockTools. Follow the… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Do Flexible Docking in AutoDock Vina (Flexible Side Chains, Step by Step) Learn how to let binding-site side chains move in AutoDock Vina: split the receptor with Meeko, run vina --flex, and judge whether… Dr. Abdul Rajjak Shaikh 14 min read Updated Molecular Modeling How to Dock Multiple Ligands in AutoDock Vina (Batch Docking): A Step-by-Step Guide Stop running Vina once per compound. Learn the --batch flag, the Open Babel prep loop, and how to pull 40 output files… Dr. Abdul Rajjak Shaikh 17 min read Updated