SDF to PDBQT
Convert SDF ligands to PDBQT with Meeko, preserving supplied coordinates.
How to convert SDF to PDBQT for ligand docking?
Upload an SDF containing 3D ligand coordinates. The SDF to PDBQT converter adds explicit hydrogens and uses Meeko to prepare AutoDock atom types, partial charges and a torsion tree. Download one or more PDBQT files per molecule. Each molecule in a multi-record SDF is prepared separately.
Meeko also converts 2D SDF records with a warning. Their supplied coordinates remain 2D; this conversion does not generate a 3D conformation for docking.
- Upload a ligand
.sdfcontaining 3D coordinates. - Leave
Meeko preparation configurationat{}for native defaults. - Run the conversion and review the result table.
- Download the
.pdbqtfiles for ligand docking.
Worked example
Input .sdf:
ethanol
RDKit 3D
9 8 0 0 0 0 0 0 0 0999 V2000
-0.9535 0.0478 0.0425 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4879 -0.3215 -0.1890 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2770 0.3248 0.7377 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3570 0.7340 -0.7332 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5933 -0.8626 0.0218 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0710 0.5964 1.0112 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7874 -0.1406 -1.2358 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5900 -1.4261 -0.0440 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8325 1.0478 0.3890 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
1 4 1 0
1 5 1 0
1 6 1 0
2 7 1 0
2 8 1 0
3 9 1 0
M END
$$$$Actual .pdbqt output:
REMARK SMILES CCO
REMARK SMILES IDX 1 1 2 2 3 3
REMARK H PARENT 3 4
ROOT
ATOM 1 C UNL 1 -0.954 0.048 0.043 1.00 0.00 0.034 C
ATOM 2 C UNL 1 0.488 -0.322 -0.189 1.00 0.00 0.152 C
ENDROOT
BRANCH 2 3
ATOM 3 O UNL 1 1.277 0.325 0.738 1.00 0.00 -0.397 OA
ATOM 4 H UNL 1 1.833 1.048 0.389 1.00 0.00 0.210 HD
ENDBRANCH 2 3
TORSDOF 1The blocks show the complete input and output for one ethanol molecule. Coordinates and chemistry shown here come from this conversion run.
Input
| Input | Accepted format | Requirements |
|---|---|---|
| Molecules | .sdf upload | Ligand SDF with supplied coordinates; use 3D coordinates for docking. Multiple molecule records accepted. Maximum file size: 50 MiB. |
Settings
| Setting | Default | What it does |
|---|---|---|
Meeko preparation configuration | {} | Advanced Meeko preparation settings as a JSON object. Leave {} for native defaults, including Gasteiger charges and AutoDock atom typing. Supplied coordinates are preserved; use a 3D structure for docking. |
Keep {} for ordinary preparation. Custom configuration must be valid JSON using options supported by Meeko 0.7.1; Meeko warns about unsupported keys and ignores them. The Meeko documentation explains preparation concepts. This field accepts Python preparation configuration, not command-line flags.
Meeko preparation presets
Use Presets, beside the Meeko preparation configuration label, to fill the JSON field:
| Preset | What changes |
|---|---|
| Standard preparation | Uses Meeko defaults, including Gasteiger charges and AutoDock atom typing. |
| Keep all hydrogens | Sets merge_these_atom_types to [], keeping all hydrogens explicit in PDBQT. |
| Rigid macrocycles | Sets rigid_macrocycles to true, keeping large rings in their supplied or generated conformation during docking. |
Selecting a preset replaces the current JSON configuration. You can edit the JSON afterward; configurations that do not match a preset display as Custom. These presets change ligand preparation, not protonation or stereoisomer enumeration.
Results
| Output | Contents |
|---|---|
| Results table | Name, SMILES, Atoms, Output file. |
molecule_1_1.pdbqt | Prepared ligand with atom types, charges, chemical remarks and torsion information. |
results.tsv | Tab-separated table with the same rows and values. |
report.json | Result rows, resolved settings and warnings. |
run.log | Tool, settings, result count and warnings; failures include their error. |
Downloads are available from Files. Inspect both the structure preview and the chemical content of the downloaded file.
What changes when SDF becomes PDBQT?
SDF stores connectivity, bond orders, optional properties and coordinates. PDBQT adds the AutoDock atom types, partial charges and rotatable-bond tree used in docking. Conversion includes ligand preparation, not merely renaming the extension.
Meeko defaults to Gasteiger charges and its native atom-typing rules. Some explicit hydrogens are merged, so a PDBQT can have fewer atom lines than the SDF or the molecule's Atoms count in the table. Chemical remarks retain information needed for later reconstruction.
The input chemical state is used rather than selecting a pH-dependent state. Use Dimorphite-DL before coordinate generation when alternatives are needed. A prepared ligand is only one docking input: the receptor, search box and docking calculation are separate.
Which docking converter should I use?
| Input available | Tool | Coordinate handling |
|---|---|---|
| 3D ligand SDF | SDF to PDBQT | Uses supplied coordinates. |
| Ligand SMILES | SMILES to PDBQT | Generates a conformer before preparation. |
| Meeko-prepared PDBQT poses | PDBQT to SDF | Reconstructs ligand pose records. |
FAQ
Can I convert a 2D SDF to PDBQT?
Yes. Meeko converts 2D coordinates with a warning, but the resulting PDBQT still contains those coordinates. For docking, generate a 3D conformation with SMILES to SDF, or start directly from SMILES with the converter above.
Does a multi-molecule SDF produce one PDBQT?
Each molecule is prepared independently. Each preparation output receives its own file, identified in the table.
Does the converter fix incorrect ligand chemistry?
No. Invalid or unpreparable structures fail explicitly. Check bond orders, charge and stereochemistry before preparation.
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