Prepare SDF and MOL ligand structures as flexible AutoDock PDBQT files with atom types, partial charges, and torsion trees. Learn more
How to convert SDF to PDBQT
Upload an SDF or MOL file, choose how to handle hydrogens and partial charges, then select Convert. ProteinIQ uses Open Babel in the browser and returns one flexible AutoDock PDBQT file per molecule. Multi-record SDF libraries keep their input order, and nothing is uploaded to a server. Each record must contain one connected ligand; remove salts and counterions before conversion.
This one-atom water molfile:
water
ProteinIQ
1 0 0 0 0 0 999 V2000
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
M ENDproduces the following PDBQT with the default polar-hydrogen and Gasteiger-charge settings:
REMARK Name = water
REMARK 0 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 O HOH 1 0.000 0.000 0.000 0.00 0.00 -0.410 OA
ATOM 2 H HOH 0 0.000 0.000 0.000 0.00 0.00 +0.205 HD
ATOM 3 H HOH 0 0.000 0.000 0.000 0.00 0.00 +0.205 HD
ENDROOT
TORSDOF 0The charge and atom-type columns are part of PDBQT preparation. They are not present in an ordinary PDB file.
Input
| Format | Accepted input |
|---|---|
.sdf, .sd | V2000 or V3000 Structure Data Files containing up to 200 molecules. Standalone $$$$ lines separate records. |
.mol | A single MDL molfile using the same atom and bond representation as an SDF record. |
| Pasted text | SDF or MOL content entered directly after switching from file upload to text input. |
The maximum uploaded file size is 50 MB. Empty or malformed records are reported with their record number instead of being silently skipped.
Preparation settings
| Setting | Default | Effect |
|---|---|---|
Hydrogens | Add polar hydrogens | Adds polar hydrogens before PDBQT writing. Use input polar hydrogens does not add missing atoms. Open Babel's PDBQT writer omits non-polar hydrogens. |
Partial charges | Assign Gasteiger charges | Calculates Gasteiger partial charges for the PDBQT charge field. Do not assign partial charges can leave charge values zero or unspecified. |
pH correction | Off | Applies Open Babel protonation correction at a numeric pH before hydrogen addition. The submitted chemical state still determines the starting molecule. |
Generate 3D coordinates | Off | Builds a new three-dimensional geometry. Leave this off to preserve coordinates already present in the SDF. |
Generating 3D coordinates rebuilds the conformation. If the input already contains nonzero Z coordinates, ProteinIQ warns before returning the regenerated structure. Coordinate generation provides a starting geometry, not a predicted bound pose or a conformer search.
Results
| File | Contents |
|---|---|
name.pdbqt | One flexible AutoDock PDBQT structure containing coordinates, partial charges, AutoDock atom types, and a torsion tree. |
name-1.pdbqt, name-2.pdbqt, ... | Individual structures from a multi-record SDF, in submitted order. |
name-conversion-log.txt | Selected preparation settings, molecule and file counts, warnings, and Open Babel runtime output. |
The Open Babel PDBQT writer emits a flexible torsion tree by default. ROOT, BRANCH, ENDBRANCH, and TORSDOF records describe which ligand bonds can rotate during docking. A rigid molecule can have TORSDOF 0 and no branch records.
Disconnected salts, counterions, and solvent fragments would produce multiple ligand trees in one PDBQT file, which is not a valid single flexible ligand for common AutoDock workflows. The converter rejects those records and identifies their record number so you can select the intended ligand first.
What changes when SDF becomes PDBQT
SDF stores molecular connectivity, bond orders, formal charges, stereochemical annotations, and optional data fields. PDBQT is designed for AutoDock-family docking programs. It combines PDB-like coordinates with a partial-charge field, AutoDock atom types, and a rotatable-bond tree.
Conversion therefore prepares a docking representation rather than making a lossless copy. SDF property fields are not carried into PDBQT, and the PDBQT torsion tree does not preserve every SDF bond-order or stereochemical annotation. Keep the original SDF as the authoritative chemical record.
Open Babel's PDBQT format documentation defines the writer behavior and available record modes. ProteinIQ runs the pinned Open Babel 3.1.0 browser build already used by the Open Babel format converter.
Is the output ready for AutoDock Vina?
The output contains the fields AutoDock-family programs expect, including atom types, partial charges, and a torsion tree. It is suitable for workflows that accept Open Babel-prepared ligands. Preparation does not prove that the submitted tautomer, protonation state, stereochemistry, or conformation is appropriate for a particular target.
For a complete docking run, submit the original SDF or a prepared PDBQT directly to AutoDock Vina. ProteinIQ's Vina workflow uses its own pinned Meeko preparation path when it prepares an SDF ligand, so its generated ligand PDBQT can differ from this Open Babel conversion.
Which converter should I use?
| Goal | Tool |
|---|---|
| Convert an SDF ligand for AutoDock-family input | SDF to PDBQT Converter |
| Convert SDF to a broadly viewable coordinate file | SDF to PDB |
| Choose from the full Open Babel format and force-field option catalog | Open Babel format converter |
| Prepare and dock a ligand against a receptor | AutoDock Vina |
FAQ
Does SDF to PDBQT add charges?
Yes. The default assigns Gasteiger partial charges. Do not assign partial charges skips that calculation; an SDF formal charge is not the same as a PDBQT per-atom partial charge, so output values can be zero or unspecified.
Does the converter add hydrogens?
It adds polar hydrogens by default. You can instead use polar hydrogens already present in the input. Open Babel's PDBQT writer omits non-polar hydrogens in both modes.
Can one SDF file contain multiple ligands?
Yes. Each SDF record becomes a separate numbered PDBQT file, up to 200 molecules per conversion. Record order is preserved.
Does converting SDF to PDBQT generate 3D coordinates?
Not by default. Existing coordinates are preserved. Enable Generate 3D coordinates only when the source is two-dimensional or lacks a usable geometry.
Are PDB and PDBQT the same format?
No. PDB stores coordinates and optional connectivity, while PDBQT adds partial charges, AutoDock atom types, and ligand torsion-tree records. Renaming a .pdb file to .pdbqt does not create those fields.
