Topic
Molecular Modeling
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 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 Dock a Peptide to a Protein (HPEPDOCK, HADDOCK and AutoDock CrankPep): A Step-by-Step Guide Learn peptide-protein docking step by step with HPEPDOCK, HADDOCK and AutoDock CrankPep, and find out which one to run for your project. 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 Molecular Modeling How to Set Protonation States and Add Hydrogens to a Protein Before Docking or MD (PDB2PQR, PROPKA and H++) Crystal structures ship without hydrogens. Learn to predict pKa values with PROPKA, protonate with PDB2PQR or H++, and check the result before… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Run GROMACS on an HPC Cluster with SLURM: Job Scripts, Modules and Restarts Move your GROMACS run from a laptop to a shared cluster. Load the right module, write a correct sbatch script, and restart… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Run an MD Simulation of a Vaccine Construct-TLR Complex in GROMACS: Setup, Length and What to Report Take a docked vaccine construct into GROMACS: which pose to carry forward, force field and box setup, how many replicas to run,… Ragini Mishra 17 min read Molecular Modeling How to Install PyMOL for Free (Open-Source PyMOL on Windows, Linux and Mac): A Step-by-Step Guide for Students Open-source PyMOL is free under a BSD-like licence. Install it with one conda command on Windows, Linux or Mac, then verify it… Dr. Abdul Rajjak Shaikh 13 min read