Tag
Protein Preparation
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 Generate a GROMACS Topology with pdb2gmx: A Step-by-Step Beginner’s Guide Learn to run gmx pdb2gmx step by step, pick a force field and water model, and fix the "residue not found" error… Dr. Abdul Rajjak Shaikh 8 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