Tag
GROMACS
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 Analyze Protein-Ligand Interactions Over an MD Trajectory (ProLIF and MDAnalysis, Step by Step) Compute which binding-site residues held your ligand and for what percentage of the run, using ProLIF and MDAnalysis on a PBC-corrected GROMACS… Dr. Abdul Rajjak Shaikh 11 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 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