Guides and tutorials
Computational life sciences, explained step by step.
Real commands, real parameters, and the errors that actually catch people out. Written by researchers who use these tools.
Molecular Modeling Meeko Tutorial: Prepare Ligands and Receptors for Vina Prepare ligands and receptors for AutoDock Vina with Meeko. Learn mk_prepare_ligand, mk_prepare_receptor and mk_export with real commands and fixes. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Ramachandran Plot from a GROMACS Trajectory (gmx rama) Learn to run gmx rama on an MD trajectory, plot every frame as a phi/psi density in Python, and spot residues that… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Extract a Ligand from a PDB File (PyMOL, ChimeraX) Pull the bound ligand out of a PDB complex, restore its bond orders and hydrogens, and use it to centre your docking… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling GNINA Docking Tutorial: CNN Scoring After AutoDock Vina Run your first GNINA docking job, read CNNscore and CNNaffinity correctly, and rescore your Vina poses. Follow the step-by-step commands. Dr. Abdul Rajjak Shaikh 14 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 76 Close by 26 October 2026 Seventy-six funding deadlines close by 26 October 2026, seventeen of them on 15 October. New this week: five Aarhus PhD calls, six… Dr. Abdul Rajjak Shaikh 64 min read Molecular Modeling GROMACS Protein Cofactor Simulation: Heme, NAD+ and FAD Keep heme, NAD+ or FAD in your GROMACS run: check the force field first, then parameterize only what is missing. Follow the… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Salt Bridge Analysis in GROMACS: gmx saltbr vs pairdist Track a salt bridge across a GROMACS trajectory with gmx pairdist, compute its occupancy in Python, and learn why gmx saltbr misleads.… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling gmx hbond for Protein-Ligand H-Bonds in GROMACS 2024+ Count protein-ligand hydrogen bonds with the new gmx hbond in GROMACS 2024+, or hbond-legacy. Copy the exact commands, get occupancy and read… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Ligand RMSD in GROMACS: Fit, Fix PBC, Read the Plot Calculate ligand RMSD in GROMACS the right way: fit on the protein backbone, fix periodic jumps first, and learn to read stable,… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling Covalent Docking Tutorial: Dock a Covalent Inhibitor AutoDock Vina cannot dock covalent inhibitors. Compare the free routes, run a covalent job in ADFR step by step, and validate the… Dr. Abdul Rajjak Shaikh 16 min read Updated
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