PDB to MOL2 Converter

How to convert PDB to MOL2

Paste or upload a PDB file, or fetch a structure by PDB ID. ProteinIQ runs Open Babel in the browser and returns its native Tripos MOL2 output. Explicit CONECT records are preserved when present; otherwise Open Babel infers connectivity, bond orders, SYBYL atom types, and Gasteiger charges from the available PDB data.

For this two-atom ligand:

HETATM    1  C1  UNL A   1       0.000   0.000   0.000  1.00 20.00           C
HETATM    2  O1  UNL A   1       1.400   0.000   0.000  1.00 20.00           O
CONECT    1    2
CONECT    2    1
END

Open Babel returns:

@<TRIPOS>MOLECULE
*****
 2 1 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1  C1         0.0000    0.0000    0.0000 C.3     1  UNL1        0.2175
      2  O1         1.4000    0.0000    0.0000 O.3     1  UNL1       -0.2175
@<TRIPOS>BOND
     1     1     2    1

This is a chemistry inference, not a lossless rewrite. PDB records coordinates and may include connectivity, but it usually does not contain the complete bond-order, protonation, atom-typing, or partial-charge information expected by MOL2 consumers. Inspect the result before using it for docking, force-field assignment, or simulation.

Input

The converter stops before Open Babel runs when coordinate fields are malformed. It also rejects duplicate atom identities, unresolved alternate conformers, and PDB insertion codes because emitting multiple coordinates for one atom or collapsing insertion-coded residues would make the MOL2 ambiguous. Select one coordinate record per atom and renumber insertion-coded residues before conversion.

The 20,000-atom ceiling bounds browser memory and bond-perception time. For a larger assembly, reduce the structure to the chains, ligand, or binding site that the next calculation needs, or run Open Babel locally.

Settings

There are no scientific settings. The page uses one fixed, auditable conversion path: PDB input, native coordinates and hydrogens, Open Babel chemistry perception, Gasteiger charges, and MOL2 output. Chain removal, water removal, protonation changes, and structure preparation should be completed explicitly before conversion.

Results

The result warning remains visible above the output to remind downstream users that chemistry absent from the PDB was inferred.

Why PDB to MOL2 can be incomplete

PDB was designed around macromolecular coordinates. Its CONECT records can identify bonded atom pairs, particularly for heterogens, but many files omit them and conventional PDB connectivity does not reliably encode aromaticity or complete bond order. MOL2 expects an explicit molecular graph, SYBYL atom types, and per-atom charges.

Open Babel fills that gap using its established PDB reader, residue templates, distance-based connectivity, and bond-order perception. This is more complete than copying coordinates or writing every perceived bond as a single bond, but it cannot recover chemistry that is genuinely ambiguous from the source file. A chemically curated SDF or existing MOL2 remains the better source for a ligand when one is available.

Large proteins deserve extra care. A whole-protein MOL2 is not automatically parameterized for AMBER, CHARMM, OPLS, or another force field, and Gasteiger charges are not a substitute for force-field-specific preparation. Convert only when the receiving program explicitly needs MOL2, and use its recommended preparation workflow afterward.

Which converter should I use?

FAQ

Can PDB to MOL2 convert a whole protein?

It can convert a structure containing up to 20,000 atoms, but the resulting MOL2 is a format conversion, not a force-field-ready protein. Large assemblies should usually be reduced to the component required by the next program.

Does PDB to MOL2 preserve CONECT records?

Yes. Open Babel reads explicit PDB connectivity. When connectivity or bond order is absent, it uses residue information and molecular geometry to infer the missing graph.

Are MOL2 bond orders guaranteed to be correct?

No. Open Babel can recognize common chemistry, including aromatic rings, but a PDB file may not contain enough information to resolve unusual ligands, metals, covalent modifications, or protonation-dependent groups. Verify those cases against a curated chemical record.

What charges are written to the MOL2 file?

The conversion requests Open Babel Gasteiger partial charges, and the MOL2 charge type is reported as GASTEIGER. These are general-purpose inferred charges, not charges prepared for a particular docking engine or molecular-mechanics force field.

Why was my alternate-location PDB rejected?

A MOL2 file should describe one coordinate state. Select one PDB alternate conformer before conversion so atoms from different states are not combined into the same molecular graph.

Why are insertion codes rejected?

The Open Babel MOL2 output does not preserve insertion codes unambiguously in residue labels. Renumber those residues first so distinct PDB residues cannot collapse to the same MOL2 identity.