MOL2 to PDBQT Converter for AutoDock Vina

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

PDBQT columns Vina reads

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.