Topic
Molecular Modeling
Molecular Modeling Protein-Ligand Interaction Energy in GROMACS (Rerun Guide) Compute Coulomb and LJ protein-ligand interaction energy in GROMACS with energygrps, mdrun -rerun and gmx energy. Follow the exact commands. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling gmx make_ndx Tutorial: Index Groups for Protein-Ligand MD Build Protein_LIG, ligand heavy-atom and pocket index groups with gmx make_ndx, script them, and fix the grompp group errors. Follow each step. Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling Set Up WSL2 for GROMACS, Vina and Open Babel Install WSL2 on Windows and get GROMACS, AutoDock Vina and Open Babel running in one Ubuntu shell. Follow every command, path and… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling MODELLER Tutorial: Build a Homology Model Step by Step Install MODELLER, pick a template, write the align2d alignment, run AutoModel and rank your models by DOPE score, using the official tutorial… Dr. Abdul Rajjak Shaikh 16 min read Molecular Modeling How to Calculate Protein-Protein Binding Affinity Score your docked protein-protein complex with PRODIGY and HawkDock MM/GBSA, read dG and Kd correctly, and learn why a docking score is… Dr. Abdul Rajjak Shaikh 12 min read 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 How to Predict a Protein-Protein Complex with AlphaFold-Multimer in ColabFold (Step by Step) Learn how to model a protein-protein complex free in ColabFold, set the chain break correctly, and judge ipTM, pTM and PAE before… Dr. Abdul Rajjak Shaikh 13 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