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PDBQT to PDB and SDF Converter for Vina Results

In short: Paste or upload the out.pdbqt file from AutoDock Vina. See every pose with its binding affinity, pick one, and download it as PDB or SDF with bond orders. Free, in your browser, no sign-up.

Quick answer: In Vina output each pose is a MODEL block. The line REMARK VINA RESULT: -7.2 0.000 0.000 gives the affinity (kcal/mol) and the RMSD lower and upper bounds from pose 1. PDBQT has no bonds, so bond orders come from a SMILES or are guessed from 3D geometry.

Docking output (PDBQT)

Upload .pdbqt

Ligand SMILES (optional)Restores bond orders exactly when the file has no SMILES remark.

Converted pose

Ready. Your file stays in your browser.

The example is ibuprofen prepared with the SDF to PDBQT converter, shown in three illustrative poses in Vina's output format. The scores are for demonstration, not from a real docking run.

What is in a Vina output PDBQT

MODEL 1 REMARK VINA RESULT: -7.200 0.000 0.000 REMARK INTER + INTRA: -8.855 REMARK SMILES CC(C)Cc1ccc(C(C)C(O)=O)cc1 REMARK SMILES IDX 1 9 2 8 3 10 4 7 5 1 ... ROOT ATOM 1 C5 UNL 1 10.820 -3.708 24.766 1.00 0.00 -0.048 A ... TORSDOF 5 ENDMDL MODEL 2 REMARK VINA RESULT: -6.900 1.952 2.349

Affinity: the first number after VINA RESULT, in kcal/mol. More negative is better. Poses are sorted best first.
RMSD l.b. / u.b.: distance of each pose from pose 1 in ångström. Pose 1 is 0.000 by definition.
Atoms: PDB-style coordinates plus the partial charge and AutoDock type (A, C, NA, OA, HD …). The element is taken from the type: A is carbon, NA is nitrogen, OA is oxygen, HD is hydrogen.
No bonds. PDBQT stores only the torsion tree, not bonds or bond orders. Hydrogens on carbon are missing because they were merged before docking.

How bond orders are restored

From the SMILES remark. Meeko and the MolDraw SDF/MOL2 to PDBQT converters write REMARK SMILES and REMARK SMILES IDX, and Vina 1.2 copies them into its output. The index map links every atom to the SMILES, so bonds, bond orders and charges are exact.
From a SMILES you enter. Bonds are found from distances, then the heavy atoms are matched to your SMILES graph. If the atoms or connections differ (a different protonation does not matter, a different molecule does), the page tells you.
From geometry only. Rings whose carbons are typed A get alternating double bonds; C=O, S=O, P=O, C≡N and C=C bonds are found from bond lengths and planarity; charges follow from valence. This worked for all 47 test ligands with good geometry, but it is a guess: check the result.

How to convert Vina PDBQT output to PDB or SDF

Upload the out.pdbqt that Vina wrote (or paste it). A single prepared ligand PDBQT works too.
If the file has no SMILES remark, paste the ligand SMILES to get exact bond orders.
Press Read poses. Select a pose in the table; pose 1 has the best affinity.
Choose SDF (bond orders, charges, affinity as a data field) or PDB (HETATM and CONECT records, for PyMOL or Chimera with the receptor) and download one pose or all poses.

The SDF stores vina_affinity_kcal_mol, vina_rmsd_lb and vina_rmsd_ub as data fields, so you can sort poses in RDKit, KNIME or DataWarrior.

Limitations

Non-polar hydrogens are not restored with coordinates; the SDF leaves them implicit.
Geometry-based bond orders can be wrong for strained or poorly built ligands, unusual groups, and tautomers. A SMILES fixes this.
Flexible receptor side chains in the output (BEGIN_RES … END_RES) are skipped. Macrocycle pseudo-atoms (G0, G1) are removed.
This page reads ligands. For a receptor PDBQT, use a structure viewer or the PDB tools linked below.
Docking scores are estimates from the Vina scoring function, not measured binding energies.

Frequently asked questions

How do I convert Vina out.pdbqt to PDB or SDF?

Upload or paste the out.pdbqt file Vina wrote, pick a pose in the table, choose PDB or SDF and download. You can download one pose or all poses. Everything runs in your browser.

Where is the binding affinity in a Vina PDBQT file?

Each MODEL block starts with REMARK VINA RESULT followed by three numbers: the affinity in kcal/mol, then the RMSD lower bound and upper bound in ångström from the best pose. Pose 1 has the lowest (best) affinity.

Why does the SDF have no hydrogens on carbon?

PDBQT files keep only polar hydrogens; hydrogens on carbon were merged into their carbons during ligand preparation. The SDF keeps them implicit. RDKit, Open Babel or PyMOL can add them back with 3D coordinates.

Are the bond orders correct?

PDBQT has no bonds or bond orders. If the file has a SMILES remark (written by Meeko or by the MolDraw converters) or you paste the ligand SMILES, bond orders are restored exactly. Otherwise they are guessed from 3D geometry and AutoDock types, and the page says so.

What do RMSD l.b. and u.b. mean?

They compare each pose with the best pose. The upper bound matches atoms one to one. The lower bound matches each atom to the nearest atom of the same type, so it ignores symmetry swaps and is smaller.

Last updated: October 30, 2026