No MGLTools required · Dock tools
PDB to PDBQT Online
Convert PDB, SDF, or SMILES to AutoDock Vina PDBQT in your browser — skip MGLTools crashes and conda installs.
Drop a molecule file here
or click to browse · .smi / .sdf / .mol / .pdb · conversion stays local
First run downloads the Open Babel engine once, then converts with Gasteiger charges in memory.
Conversion result
Successful conversions auto-download a .pdbqt file. A summary appears here afterward.
How to convert PDB to PDBQT online (also SDF / SMILES)
Searching for PDB to PDBQT online or “convert without MGLTools”? AutoDock Vina expects PDBQT — coordinates plus partial charge (Q) and AutoDock atom type (T). This free converter runs Open Babel WebAssembly in your browser so you can skip MGLTools, conda, and command-line obabel for routine teaching and early screening prep.
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Choose input format (or Auto-detect)
Select SMILES, SDF, MOL, MOL2, or PDB — or leave Auto-detect. Upload a file or paste structure text. Pair drug names with our Name to SMILES tool first if you only have an IUPAC or trade name.
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Convert in the browser with Open Babel
On first use we load the Open Babel engine (~8 MB). SMILES get 3D embedding when needed; hydrogens are added at pH 7.4; Gasteiger charges and AutoDock atom types are written into PDBQT.
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Download .pdbqt and dock
The file downloads automatically for local Vina/Smina scripts. Or click Format Ready! Start Cloud Docking to run Meeko + AutoDock Vina online on Dock with a PDF/ZIP report.
What is PDBQT and why does AutoDock Vina need it?
PDBQT extends the familiar PDB atom table with two docking-critical fields: partial charge (Q) and AutoDock atom type (T). Vina's scoring function uses those types (and rotatable-bond roots for ligands) rather than raw element symbols alone. A plain PDB or SDF from RCSB or ChemDraw is not enough for a typical local Vina command line.
Historically, students installed MGLTools / AutoDockTools or ran obabel input.sdf -O ligand.pdbqt -h. This page targets the same intent — "SDF to PDBQT online", "SMILES to PDBQT", "PDB to PDBQT converter", "convert to PDBQT without MGLTools" — with a privacy-friendly in-browser path.
For cloud jobs on Dock you can skip manual PDBQT entirely: paste a PDB ID and ligand SMILES and Meeko prepares receptor/ligand PDBQT server-side. Use this converter when you need a downloadable file for homework scripts, PyMOL inspection, or offline Vina.
Supported molecular formats for PDBQT conversion
Pick the path that matches how your structure is stored. Ligand-sized inputs are the sweet spot for browser WASM; huge crystal receptors belong in a server prep workflow.
SMILES → PDBQT
Paste a line notation (drug SMILES from PubChem or our Name to SMILES tool). Open Babel embeds 3D coordinates (MMFF94 when available), adds hydrogens at pH 7.4, assigns Gasteiger charges, and writes AutoDock atom types.
SDF / MOL → PDBQT
Upload an MDL connection table with 2D or 3D coordinates. Multi-molecule SDF files convert molecule-by-molecule into one concatenated PDBQT stream — ideal for small teaching libraries.
PDB → PDBQT
Use ligand-sized PDB excerpts or small peptides. Full crystallographic receptors often exceed browser memory; clean waters first with the PDB Cleaner, or run receptor prep in Dock's cloud Meeko pipeline.
MOL2 → PDBQT
Tripos MOL2 (common from docking exports and some force-field tools) is accepted when you need to re-type atoms for AutoDock Vina without installing MGLTools.
Try example SMILES → PDBQT
Click a familiar compound to paste its SMILES and run the live converter — useful for demos, lab onboarding, and verifying that downloads work before your own library.
| Compound | Typical use | What to expect |
|---|---|---|
| Minimal tutorial ligand | Tiny PDBQT — good first smoke test | |
| Classic oral drug example | Small organic with ester + acid | |
| NSAID coursework ligand | Flexible side chain → TORSDOF in Vina | |
| Rigid heterocycle demo | Compact fused-ring PDBQT |
Open Babel vs MGLTools vs Meeko for PDBQT
All three can produce PDBQT, but they fit different stages of a docking workflow. Use this table when choosing a free online converter versus a full AutoDock Vina pipeline.
| Tool | Best for | Charges / typing | Install |
|---|---|---|---|
| This converter (Open Babel WASM) | Quick ligand SDF/SMILES → PDBQT in the browser | Gasteiger–Marsili | None (first load ~8 MB WASM) |
| MGLTools / AutoDockTools | Legacy receptor prep, flexible side chains, ADT GUI | Gasteiger (ADT) / custom | Desktop Python stack |
| Meeko (Dock cloud) | Production Vina receptor + ligand prep with TORSDOF | Meeko / AutoDock typing | None on Dock — runs server-side |
| obabel CLI | Batch scripts on a laptop or HPC | Gasteiger via --partialcharge | conda / apt Open Babel |
CLI equivalent of this page's defaults: obabel input.sdf -O out.pdbqt -h --partialcharge gasteiger; (plus --gen3d for SMILES). State the method clearly in lab reports — Gasteiger Open Babel is not identical to Meeko preparation.
Why convert to PDBQT before molecular docking?
Docking engines do not "see" a ChemDraw sketch or a raw SMILES string the way humans do. Converting to PDBQT is the handoff that adds protonation/hydrogens, partial charges, and atom typing so AutoDock Vina can evaluate steric and hydrophobic terms consistently. Skipping conversion is a common source of cryptic Vina errors in student labs.
A practical prep sequence on Dock: chemical name → SMILES, optional Lipinski Rule of 5 filter, protein name → PDB ID, clean waters / HETATM, grid box center/size, then either this PDBQT converter for local Vina or the Dock homepage for cloud AutoDock Vina with Meeko prep and a downloadable report.
Search intents this page covers include PDB to PDBQT online, SDF to PDBQT converter, SMILES to PDBQT free, molecular format converter for AutoDock, and prepare ligand for Vina without installing MGLTools.
Ligand vs receptor PDBQT — practical limits
Ligands (drug-like SMILES, SDF from vendors, co-crystal ligands exported from a pocket) convert well in-browser. Expect a short wait on first engine load, then near-instant downloads for molecules under a few hundred atoms.
Receptors (full PDB proteins) are heavier: Open Babel WASM must hold the whole polymer in memory, and AutoDock-style receptor prep often needs water removal, non-standard residue handling, and rigid vs flexible side-chain decisions. Prefer the PDB Cleaner + Dock cloud Meeko path for receptors, or a local Meeko/Open Babel install for batch apo structures.
Soft limits here: ~2.5 MB text input and ~20 000 atoms. If conversion fails on a large PDB, trim to the binding-site chains or use a serverless Open Babel API (see the example under examples/pdbqt-converter-api).
PDBQT converter FAQ
Short answers for students and researchers preparing AutoDock Vina ligands from SMILES, SDF, or PDB without installing MGLTools.
PDBQT is a PDB-like coordinate file that also stores partial charges (Q) and AutoDock atom types (T). AutoDock Vina and related engines read PDBQT for ligands and receptors instead of plain SDF/PDB alone.
Related docking tools
- Search PDB by Protein Name
Find high-resolution PDB IDs from a protein name (EGFR, ACE2, HER2) and dock in one click.
- Chemical Name to SMILES
Convert drug or IUPAC names into Canonical SMILES via PubChem — ready for AutoDock Vina.
- PDB Cleaner — Remove Water & Heteroatoms
Strip HOH waters and optional HETATM records from a PDB in your browser — docking-ready receptor prep.
- AutoDock Vina Grid Box Calculator
Upload a reference ligand PDB/SDF to compute Center X/Y/Z and Size for your Vina search box — copy config.txt in one click.
- Lipinski Rule of 5 & Drug-likeness Checker
Paste SMILES to compute MW, LogP, HBD, and HBA with RDKit.js in-browser — pass/fail Lipinski filter before docking.
- Online AutoDock Vina docking
Paste a PDB ID, add SMILES, and run cloud docking with Meeko prep and a downloadable report — no local PDBQT required.
- All free docking prep tools
Browse the full tools hub — PDB finder, name to SMILES, PDB cleaner, grid box, Rule of 5, PDBQT.