PDB to MOL2 Converter

Convert PDB structures to MOL2 with atom typing, bond detection, and partial charges.

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MOL2 to SMILES

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What's the difference between PDB and MOL2 formats?

PDB (Protein Data Bank) files store atomic coordinates for proteins, nucleic acids, and other macromolecules, often including experimental metadata and biological context.

Key features of the PDB format:

  • Fixed-width columns with specific positioning
  • ATOM records contain chain ID, residue name, and atom serial numbers
  • CONECT records explicitly define atomic bonds
  • Header information includes experimental metadata
  • Primarily designed for macromolecular structures
PDB
1HEADER    SMALL MOLECULE                          15-JUN-25   DEMO2TITLE     EXAMPLE MOLECULE - METHANOL3ATOM      1  C   UNL A   1      -0.748   0.015   0.024  1.00 20.00           C4ATOM      2  O   UNL A   1       0.667   0.015   0.024  1.00 20.00           O5ATOM      3  H   UNL A   1      -1.142  -0.505  -0.861  1.00 20.00           H6ATOM      4  H   UNL A   1      -1.142  -0.505   0.909  1.00 20.00           H7ATOM      5  H   UNL A   1      -1.142   1.035   0.024  1.00 20.00           H8ATOM      6  H   UNL A   1       0.962   0.535   0.789  1.00 20.00           H9CONECT    1    2    3    4    510CONECT    2    1    611END

MOL2 (Tripos MOL2) files contain molecular structure data with enhanced chemical information including formal charges, atom types, and substructure definitions, commonly used in computational chemistry and drug design.

Key features of the MOL2 format:

  • Human-readable ASCII format with tagged sections
  • @<TRIPOS>MOLECULE section with molecular properties
  • @<TRIPOS>ATOM section with coordinates, atom types, and formal charges
  • @<TRIPOS>BOND section defining connectivity and bond types
  • Support for multiple molecules in a single file
  • Widely used in molecular modeling software like SYBYL
mol2
1@&lt;TRIPOS&gt;MOLECULE2Methanol36 5 0 0 04SMALL5USER_CHARGES6 7@&lt;TRIPOS&gt;ATOM81 C1 -0.7480 0.0150 0.0240 C.3 1 UNL 0.145092 O1 0.6670 0.0150 0.0240 O.3 1 UNL -0.3950103 H1 -1.1420 -0.5050 -0.8610 H 1 UNL 0.0625114 H2 -1.1420 -0.5050 0.9090 H 1 UNL 0.0625125 H3 -1.1420 1.0350 0.0240 H 1 UNL 0.0625136 H4 0.9620 0.5350 0.7890 H 1 UNL 0.262514 15@&lt;TRIPOS&gt;BOND161 1 2 1172 1 3 1183 1 4 1194 1 5 1205 2 6 1

The conversion from PDB to MOL2 transforms the fixed-width PDB format into the more flexible MOL2 structure while adding chemical information like atom types, formal charges, and enhanced bond descriptions.

Common use cases for converting PDB to MOL2 include:

  • Preparing structures for molecular dynamics simulations
  • Input for QSAR modeling and drug design workflows
  • Compatibility with Tripos SYBYL and other molecular modeling packages
  • Enhanced chemical analysis with formal charge and atom type information
  • Creating ligand libraries for virtual screening campaigns

Other PDB to MOL2 conversion methods

The ProteinIQ PDB to MOL2 converter provides an efficient online solution for quick conversions without software installation, particularly valuable for researchers needing occasional format conversion with customizable atom typing and charge assignment.

Using OpenBabel (Command Line)

OpenBabel offers robust PDB to MOL2 conversion with various options:

Bash
1# Basic PDB to MOL2 conversion2obabel input.pdb -O output.mol23 4# Convert with formal charge calculation5obabel input.pdb -O output.mol2 --partialcharge gasteiger6 7# Add hydrogens during conversion8obabel input.pdb -O output.mol2 -h9 10# Batch convert multiple PDB files11obabel *.pdb -O combined.mol2

Using PyMOL

PyMOL provides both GUI and scripting options for PDB to MOL2 conversion:

Python
1# PyMOL command line2load input.pdb3save output.mol24 5# Or using PyMOL Python API with additional processing6import pymol7pymol.cmd.load("input.pdb")8pymol.cmd.h_add()  # Add hydrogens if needed9pymol.cmd.save("output.mol2")

Using RDKit (Python)

For programmatic conversion with enhanced chemical processing:

Python
1from rdkit import Chem2from rdkit.Chem import AllChem, rdMolDescriptors3 4# Read PDB file5mol = Chem.MolFromPDBFile('input.pdb')6 7if mol is not None:8    # Add hydrogens and compute partial charges9    mol = Chem.AddHs(mol)10    AllChem.ComputeGasteigerCharges(mol)11 12    # Write to MOL2 format13    writer = Chem.rdmolfiles.MolToMol2File(mol, 'output.mol2')

Using UCSF Chimera

Chimera offers a GUI-based approach with advanced molecular visualization:

text
11. File → Open → Select your PDB file22. Tools → Structure Editing → Add H (if hydrogens needed)33. Tools → Structure Analysis → Add Charges44. File → Save MOL255. Choose output location and save

Using Schrödinger Suite

For advanced molecular modeling workflows:

text
11. Open Maestro22. Import → Import Structures → Select PDB file33. Tools → Protein Preparation Wizard (if needed)44. Export → Export Structures55. Select MOL2 format and configure options66. Save to desired location

Using GOLD Suite

Specifically for drug design applications:

text
11. Load PDB structure in GOLD22. Prepare → Process Ligand33. Set atom types and formal charges44. Export → MOL2 format55. Save processed structure