How to extract text from your MOL2 file
- Click the "Select File" button above, and choose your MOL2 file.
- You’ll see a preview, if available.
- Click the "Convert file to..." button to extract text information.
Convert MOL2 to another file type
To convert your MOL2 file to another format, you need Certara SYBYL or other Data software.
- MOL2 to PDB
- MOL2 to STR
- MOL2 to CSV
- MOL2 to JSON
- MOL2 to XML
- MOL2 to YAML
- MOL2 to YML
- MOL2 to TOML
- MOL2 to INI
- MOL2 to CFG
- MOL2 to CONF
- MOL2 to DAT
Convert a file to MOL2
To convert other file formats to the "Molecular Modeling" file type, you need software like Certara SYBYL or a similar tool.
- DBF to MOL2
- XML to MOL2
- SQLITE to MOL2
- XLSX to MOL2
- SQL to MOL2
- TSV to MOL2
- ACCDB to MOL2
- YAML to MOL2
- MDB to MOL2
- CSV to MOL2
- ODS to MOL2
- JSON to MOL2
About MOL2 files
The .MOL2 file format is a complete, portable representation of a molecule, originally developed by Tripos for use with their SYBYL molecular modeling software. Unlike simpler chemical formats that only store geometry, a .MOL2 file encapsulates atom types, bond connectivity, partial charges, and centroid coordinates needed for molecular dynamics and docking simulations. While the format is text-based and human-readable, its strict reliance on Sybyl Atom Types often creates compatibility friction when moving data between different force fields or simulation engines (like AMBER or CHARMM). Users frequently encounter parsing errors if the fixed-width column formatting is slightly off or if proprietary atom types are unrecognized by third-party viewers. For broader compatibility with web viewers or crystallographic software, it is often best to convert .MOL2 files to PDB (Protein Data Bank) format or standard SDF files. For simple visualization without the force field data, converting to XYZ or OBJ is recommended.
Convert.Guru analyzes your MOL2 file, detects the exact format, and lets you read the text inside.
Users also converted MOL, PDB, SDF, PNG, JSON, XLSX, XML, JPG, GZ, KSS and STR files.
The MOL2 Converter Story
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our MOL2 converter.