
PDB to MOL2 Converter
Convert PDB protein structure files to MOL2 format for molecular modeling and drug design applications. Upload a PDB file or paste the structure data below.
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:
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 611ENDMOL2 (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:
@<TRIPOS>MOLECULE section with molecular properties@<TRIPOS>ATOM section with coordinates, atom types, and formal charges@<TRIPOS>BOND section defining connectivity and bond types1@<TRIPOS>MOLECULE2Methanol36 5 0 0 04SMALL5USER_CHARGES6 7@<TRIPOS>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@<TRIPOS>BOND161 1 2 1172 1 3 1183 1 4 1194 1 5 1205 2 6 1The 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:
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.
OpenBabel offers robust PDB to MOL2 conversion with various options:
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.mol2PyMOL provides both GUI and scripting options for PDB to MOL2 conversion:
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")For programmatic conversion with enhanced chemical processing:
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')Chimera offers a GUI-based approach with advanced molecular visualization:
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 saveFor advanced molecular modeling workflows:
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 locationSpecifically for drug design applications:
11. Load PDB structure in GOLD22. Prepare → Process Ligand33. Set atom types and formal charges44. Export → MOL2 format55. Save processed structure