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Research articles, tutorials, and practical guidance tagged PDBQT.
Find a method, workflow, scientific concept, or software decision.
Install AutoDock Vina 1.2.7 on Windows 11, verify the official EXE in PowerShell, fix path and config errors, and choose between CLI and a guided workflow.
Read the analysisFilter the publication by research area or keyword.
Evidence-led articles on scientific methods, reproducible workflows, and software decisions.
Prepare single ligands or SDF libraries for AutoDock Vina with Meeko while preserving chemical identity, state, atom mapping, validation decisions, and provenance.
Use mk_prepare_receptor to create AutoDock Vina receptor PDBQT and box files while documenting parsers, residue decisions, outputs, validation, and provenance.
Learn what a PDBQT file stores, how ligand torsion trees differ from rigid receptor records, why bond orders can be lost, and what to inspect before an AutoDock Vina run.
An SDF file can load and still be unfit for docking. Diagnose valence, aromaticity, fragments, stereochemistry, hydrogens, 3D geometry, minimization, and PDBQT failures before AutoDock Vina.
Prepare receptor and ligand inputs for AutoDock Vina with a reproducible workflow for structure selection, protonation, PDBQT generation, inspection, and preparation records.