---
title: "MOL2 to PDBQT Converter for AutoDock Vina | MolDraw"
url: https://www.moldraw.com/tools/free-chem-tools/mol2-to-pdbqt-converter.html
description: "MOL2 to PDBQT converter for AutoDock Vina: keep MOL2 charges or use Gasteiger, AD4 atom types, torsion tree. Example: aspirin MOL2 gives 4 torsions."
lang: en
publisher: Scidart Academy
generated: 2026-10-31
---
[MolDraw](https://www.moldraw.com/) › [Chemistry tools](https://www.moldraw.com/tools/) › MOL2 to PDBQT Converter

# MOL2 to PDBQT Converter for AutoDock Vina

**In short:** Upload a Tripos MOL2 ligand and get a PDBQT file ready for AutoDock Vina: MOL2 or Gasteiger charges, AutoDock atom types and a torsion tree. It runs in your browser, free, with no sign-up.

**Quick answer:** A ligand PDBQT is a PDB-style file with a partial charge and an AutoDock atom type on every atom, non-polar hydrogens merged into their carbons, and ROOT/BRANCH records for rotatable bonds. Aspirin gives 14 atoms, 4 active torsions and `TORSDOF 4`.

## Ligand MOL2 input

Upload .mol2 Examples:

## PDBQT output

Gasteiger charges (recompute, standard for AutoDock) Keep the MOL2 partial charges

Ready. Your file stays in your browser.

## What the converter does

1. **Reads the MOL2.** Every `@<TRIPOS>MOLECULE` record, its atoms (element from the SYBYL type, such as `C.ar` or `N.am`), partial charges and bonds. Ring `ar` bonds become alternating single and double bonds; `am` bonds are single. Lone pairs (`LP`) and dummy atoms are skipped. Salts and waters are removed (largest fragment kept).
2. **Formal charges.** MOL2 has no formal charge field, so charges are worked out: `N.4` is N+, a nitrogen with four bonds is N+, carboxylate and phosphate `O.co2` oxygens get one double bond and the rest are O−, and a 3-connected aromatic N that needs a double bond is pyridinium N+.
3. **Hydrogens and 3D.** A 2D file (all z = 0) gets one 3D conformer with all hydrogens, built with OpenChemLib's conformer generator and minimised with MMFF94s. A 3D file keeps its coordinates; missing hydrogens are added at standard bond lengths and angles.
4. **Partial charges.** By default Gasteiger-Marsili (PEOE) charges with RDKit's parameters, 12 iterations. Or keep the charges from the MOL2 file. Merged hydrogens add their charge to the carbon in both cases, so the total stays the same.
5. **AutoDock atom types.** Each atom gets an AutoDock 4 type (table below). Aromaticity uses the 4n + 2 rule on rings and fused rings.
6. **Merges non-polar hydrogens.** Hydrogens on carbon are removed and their charge is added to the carbon, as AutoDock expects. Polar hydrogens stay as HD.
7. **Torsion tree.** Acyclic single bonds are rotatable, except amide and amidine C–N bonds and bonds that only spin a terminal atom (for example a CH3). The central rigid group becomes ROOT; each rotatable bond opens a BRANCH. `TORSDOF` equals the number of active torsions.

We checked the output against Meeko 0.8 (the AutoDock team's ligand preparation tool, with RDKit Gasteiger charges) on 47 drug-like molecules, written as SYBYL MOL2 files with `ar`, `am` and `O.co2` records: the same AutoDock types and torsion counts, and Gasteiger charges within 0.002 e. Meeko can read the SMILES remarks this tool writes and rebuild the molecule from the PDBQT.

### AutoDock atom types

| Type | Atoms | Rule used |
| --- | --- | --- |
| `C` | Aliphatic carbon | Carbon not in an aromatic ring |
| `A` | Aromatic carbon | Carbon in an aromatic ring (benzene, pyridine, indole, caffeine rings) |
| `NA` | Nitrogen, H-bond acceptor | Default for N: pyridine N, amines, imines, nitriles |
| `N` | Nitrogen, not an acceptor | Amide N, aniline and pyrrole-type N, N bonded to an aromatic atom with three connections, charged N+ |
| `OA` | Oxygen | All oxygens (always acceptors) |
| `SA` | Sulfur, acceptor | Non-aromatic S with two connections (thioether, thiol) |
| `S` | Other sulfur | Sulfonyl, sulfoxide, thiophene S |
| `HD` | Polar hydrogen (donor) | H on N, O, S, P or F |
| `F Cl Br I P` | Halogens, phosphorus | By element |

### PDBQT columns Vina reads

ATOM 7 C7 UNL 1 -2.336 0.072 -0.907 1.00 0.00 +0.038 C 1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890123456789

x, y and z are in columns 31–54, the partial charge in columns 71–76 (Vina reads 69–76) and the AutoDock type in columns 78–79. Every line this tool writes is checked against these positions.

## How to convert MOL2 to PDBQT

1. Upload your `.mol2` file, paste it, or press an example.
2. Choose **Gasteiger charges** or **Keep the MOL2 partial charges**.
3. Press **Convert to PDBQT**. Each ligand appears in the table with its atom count, torsions, net charge and atom types.
4. Read the notes under the table. They say which charges were used and if hydrogens were added or a fragment was removed.
5. Download one `.pdbqt` per ligand and dock: `vina --receptor receptor.pdbqt --ligand ibuprofen.pdbqt --config config.txt`.

### Many ligands in one MOL2

AutoDock Vina reads **one ligand per PDBQT file**. Use the download button on each row, or **Download all** to get one file with `MODEL`/`ENDMDL` blocks. That combined file is for viewers and for splitting: run `vina_split --input all_ligands.pdbqt` to get one file per ligand, then dock them one by one or with `vina --batch` (Vina 1.2). Do not pass the combined file to `--ligand`.

## Limitations

- **MOL2 files differ.** Programs write SYBYL types and bond types in slightly different ways. Formal charges are inferred from types and valence, so check the net charge in the table. If hydrogens are missing they are added and the MOL2 charges are replaced by Gasteiger charges, because the old charges no longer add up.
- **Protonation is not predicted.** The tool uses the protonation in your file. Neutral carboxylic acids stay neutral, amines stay neutral. Set the protonation state at your pH before converting, for example with the protonation tool linked below.
- **Gasteiger charges are approximate.** They follow RDKit and match Meeko to about 0.002 e, but MGLTools or Open Babel can differ in the second decimal. AutoDock Vina's scoring function does not use partial charges; they matter for AutoDock 4.
- **One conformer for 2D input.** Ring shapes (chair, boat) come from that conformer and stay fixed during docking. Start from a good 3D structure when ring conformation matters.
- **Rings are rigid.** Meeko can make rings of 7 or more atoms flexible with G0/CG pseudo-atoms; this tool does not (same as `mk_prepare_ligand.py --rigid_macrocycles`).
- **Ligands only.** Elements C, H, N, O, F, P, S, Cl, Br and I. Metals and boron are refused. For a receptor use the PDB to PDBQT page and a receptor preparation tool.
- Up to 200 heavy atoms per ligand and 500 ligands per run.

## Frequently asked questions

### Should I keep the MOL2 charges or recompute Gasteiger charges?

Keep the MOL2 charges when they come from a better method (for example AM1-BCC from Antechamber or charges from a force field) and you will use AutoDock 4 scoring. Recompute Gasteiger to match the usual AutoDock workflow. AutoDock Vina's scoring function does not use partial charges, so for Vina the choice does not change the score.

### How are MOL2 aromatic (ar) and amide (am) bonds handled?

Aromatic ring bonds are turned into alternating single and double bonds. Amide bonds are single bonds that stay rigid in the torsion tree. Non-ring ar bonds of carboxylates, phosphates and nitro groups are read as one double bond plus negatively charged oxygens.

### Does Vina accept a MOL2 file directly?

No. AutoDock Vina reads ligands only as PDBQT, one ligand per file. Convert the MOL2 here and download one .pdbqt per ligand. A MOL2 with several molecules gives several PDBQT files.

### Which AutoDock atom types are used?

C for aliphatic carbon, A for aromatic carbon, NA for nitrogen acceptors, N for amide, aniline, pyrrole and charged nitrogens, OA for oxygen, SA for thioether and thiol sulfur, S for other sulfur, HD for hydrogens on N, O or S, plus F, Cl, Br, I and P.

### How many torsions will my ligand have?

Every acyclic single bond that moves atoms is active, except amide and amidine C-N bonds. Aspirin has 4, ibuprofen has 5 and imatinib has 7. Ring bonds stay rigid.

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Last updated: October 30, 2026