Tutorials.
Each tutorial lists the exact software versions it was written against, shows the commands and what the output should look like, and collects the errors people actually hit, with fixes. Essays, overviews and paper notes are under Notes. Entries below are in technical review and currently noindex.
Computational chemistry
ISB-0001Chem Redocking with AutoDock Vina 1.2 and Meeko: a reproducible 1HSG walkthrough Prepare receptor and ligand with Meeko, define the box, dock with Vina 1.2.7, and validate by redocking indinavir into HIV-1 protease (PDB 1HSG). AutoDock Vina 1.2.7 · Meeko 0.8.0 · RDKit 2026.03.1 · Open Babel 3.2.1 · Python 3.12 beginner Docking · 7 min ISB-0002Chem Choosing GROMACS .mdp parameters: a stage-by-stage guide for GROMACS 2026 What every line of an EM, NVT, NPT and production .mdp file does, which defaults to trust, and the force-field-specific settings that matter. GROMACS 2026.3 intermediate Molecular dynamics · 6 min ISB-0003Chem Common GROMACS errors and how to fix them (2026 edition) Real grompp, pdb2gmx and mdrun error messages from GROMACS 2026.3, what causes each one, and the fix. No -maxwarn shortcuts. GROMACS 2026.3 beginner Troubleshooting · 6 min ISB-0004Chem Protein–ligand MD in GROMACS 2026 with AMBER99SB-ILDN and GAFF2 (ACPYPE): HIV-1 protease + indinavir A tested protein–ligand MD setup in GROMACS 2026.3: GAFF2/AM1-BCC ligand via ACPYPE, topology merging, solvation, ions, EM, NVT, NPT, production and analysis. GROMACS 2026.3 · ACPYPE 2026.10.15 · AmberTools 26.0 · RDKit 2026.03.1 · Open Babel 3.2.1 intermediate Molecular dynamics · 9 min ISB-0005Chem MM-GBSA and MM-PBSA with gmx_MMPBSA 1.7: a tested workflow and how to read the numbers End-state binding energies from a GROMACS trajectory with gmx_MMPBSA 1.7.0: inputs, GB vs PB, dielectric, decomposition, entropy, and how to read the numbers. gmx_MMPBSA 1.7.0 · AmberTools 26.0 · GROMACS 2026.3 · ParmEd 4.3.1 · Python 3.12 intermediate Free energy · 9 min ISB-0006Chem How to Curate and Classify Bioactivity Data From ChEMBL How a ChEMBL IC50 table for one target becomes a labelled set: one row per molecule, a mean potency, and a class that leaves the uncertain middle out. beginner Data curation · 4 min ISB-0007Chem Using PaDELPy to Generate Molecular Fingerprints for Machine-Learning QSAR Turn a SMILES table into PaDEL fingerprints and a random forest, then score a held-out split with Matthews correlation. The CV number is computed, not assumed. beginner QSAR · 4 min