SMILES to PDBQT Converter
In short: Convert a SMILES string into PDBQT format for molecular docking and AutoDock-style workflows. It is free, works in your web browser and needs no download.
Convert SMILES to PDBQT in two steps: generate a 3D PDB from SMILES, then transform the structure into PDBQT text for docking-ready workflows.
Input and output formats
| Input: SMILES | Output: PDBQT | |
|---|---|---|
| Full name | SMILES (Simplified Molecular Input Line Entry System) | PDBQT (AutoDock format) |
| What it holds | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. | PDB coordinates plus partial charges (Q) and AutoDock atom types (T), with torsion data for ligands. |
| File or form | .smi or plain text | .pdbqt |
Technical Workflow
- Step 1: the tool requests 3D PDB coordinates from a public SMILES conversion endpoint.
- Step 2: PDB atom lines are rewritten into PDBQT-style records with atom type and charge columns.
- Use this quick converter for drafts; fine-tune protonation and torsion settings in docking software when needed.
File Format Explained
SMILES is a compact connectivity string. It is good for describing a ligand quickly, but it does not contain docking atom types, charges, torsions, or 3D coordinates.
PDBQT is an AutoDock-style docking format. It stores PDB-like coordinates plus partial charge and AutoDock atom type fields, and ligand files may include torsion tree records such as ROOT, BRANCH, ENDBRANCH, and TORSDOF.
This converter creates a browser-side PDBQT draft. For production AutoDock Vina docking, review hydrogens, protonation, charge model, atom typing, and rotatable bonds.
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