Topic
Molecular Modeling
Molecular Modeling How to Write the Methods Section for a Molecular Dynamics Study (GROMACS Example) Turn your GROMACS run into a methods section a reviewer cannot reject. The exact parameters to report, real citations, and a worked… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling How to Make Publication-Quality Figures in PyMOL: Protein-Ligand Complexes, Step by Step Turn a docked pose into a figure your supervisor accepts. Real PyMOL commands for cartoon-plus-sticks, labelled H-bonds, and a 300 dpi ray-traced… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling The GROMACS .mdp File Explained: The Parameters That Actually Matter Stop copy-pasting em.mdp and md.mdp. Learn which GROMACS .mdp parameters you must choose deliberately, which to leave at defaults, and what breaks… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling Common GROMACS Errors and How to Fix Them (LINCS Warnings, PBC and ‘Atom Not Found’) Decode the GROMACS errors beginners actually hit: LINCS warnings, PBC artifacts, rtp mismatches and cut-off failures. Read the fix for each message. Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Calculate Protein-Ligand Binding Free Energy in GROMACS (MM-PBSA Tutorial) Estimate protein-ligand binding free energy from a finished GROMACS trajectory with the free gmx_MMPBSA tool. Follow the step-by-step MM-PBSA workflow now. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Do Blind Docking with AutoDock Vina When You Don’t Know the Binding Site Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses.… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling AlphaFold vs Homology Modelling vs Experimental Structures: Which to Use, When Learn to choose between an experimental PDB structure, a SWISS-MODEL homology model, or AlphaFold for docking and MD, judged on coverage, confidence… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Prepare a Protein Structure for MD Simulation (Missing Residues, Hydrogens, Protonation) Learn to clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling How to Validate a Protein Structure: Ramachandran Plots and MolProbity Scores Explained Validate your AlphaFold or homology model with a Ramachandran plot and MolProbity before you waste compute on docking. Learn every score and… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling Homology Modelling Tutorial for Beginners: Build a Protein Structure with SWISS-MODEL (Step by Step) Build a 3D protein model from sequence with SWISS-MODEL, no install. Learn to pick a template and read GMQE and QMEANDisCo before… Dr. Abdul Rajjak Shaikh 11 min read Updated