Topic
Molecular Modeling
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 UCSF ChimeraX Tutorial for Beginners: Load, Inspect and Clean a Protein Structure Learn UCSF ChimeraX in one sitting: fetch a PDB entry, master the 12 core commands, then clean the structure for docking or… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Calculate a Binding Free Energy with Umbrella Sampling in GROMACS (Pulling, Windows and gmx wham) Learn how to run umbrella sampling in GROMACS: set up the pull code, pick windows that overlap, run gmx wham and read… Dr. Abdul Rajjak Shaikh 18 min read Updated Molecular Modeling How to Analyze a GROMACS Trajectory in Python with MDAnalysis: A Step-by-Step Guide for Beginners Load a GROMACS .tpr and .xtc into MDAnalysis, reproduce RMSD and RMSF in Python, and write the per-frame analysis no gmx tool… Dr. Abdul Rajjak Shaikh 20 min read Updated Molecular Modeling How to Analyze Protein Secondary Structure from a GROMACS Trajectory (gmx dssp): A Step-by-Step Guide Run gmx dssp on your GROMACS trajectory, read the .dat and .xvg outputs, and fix the "do_dssp not found" error that breaks… Dr. Abdul Rajjak Shaikh 13 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 Molecular Modeling How to Predict the Effect of a Mutation on Protein Stability (DynaMut2, mCSM and DDMut): A Step-by-Step Guide Predict how a point mutation changes protein stability with DynaMut2, mCSM and DDMut, and learn to read the ddG sign correctly before… Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How to Do Protein-Protein Docking Online (ClusPro, HDOCK and HADDOCK): A Step-by-Step Guide for Beginners Dock two proteins in a browser with ClusPro, HDOCK or HADDOCK. Prepare your files, run the job, and learn which model to… Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How to Make a Point Mutation in a Protein Structure and Compare It with the Wild Type (PyMOL Mutagenesis + GROMACS) Mutate a residue in PyMOL, save the mutant correctly, then run a fair wild-type vs mutant MD comparison in GROMACS without overclaiming… Dr. Abdul Rajjak Shaikh 14 min read Updated Molecular Modeling How to Set Up a Membrane Protein MD Simulation with CHARMM-GUI and GROMACS Build a protein-in-bilayer system with CHARMM-GUI Membrane Builder, then run the six-step equilibration ladder in GROMACS without rebuilding anything. Dr. Abdul Rajjak Shaikh 13 min read Updated