Open Babel Online Converter

Molecular File Converter

Convert between chemical file formats with our web-based tool powered by Open Babel

Convert Molecular Files

Input Format

Output Format

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Supports PDB, SDF, MOL2 and many more

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Comprehensive Formats

Convert between PDB, SDF, MOL2, SMILES, and 100+ other formats.

High Performance

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Files are processed securely and deleted from our servers after 5 minutes.

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Our Open Babel Online Converter is a powerful and versatile web utility that is the ultimate chemical translator for computational chemists, molecular modelers, and bioinformaticians. Powered by the renowned Open Babel chemical toolbox, this tool facilitates seamless interoperability between hundreds of different software packages by converting between over 100 chemical file formats.

Input Format Category	Data Type & Information	Example Formats
Line Notations	Simplified Molecular Representation (Connectivity, Isomers)	`smiles`, `inchi`, `smi`
2D/3D Structures	Atomic Coordinates, Connectivity, Metadata	`pdb`, `mol`, `mol2`, `sdf`, `xyz`
QM/MM Packages	Energy, Geometry, Orbitals, Force Fields	`gaussian`, `gamess`, `mopac`, `charmm`

How to use (step-by-step)

Follow these simple steps to convert your chemical files in seconds.

Provide Input Data: Click “Upload File” or drag and drop your file. You can also directly paste the content of a file (e.g., a SMILES string) using the “Paste Data” option.
Specify Formats: Use the extensive “Input Format” and “Output Format” dropdown menus to select the formats you want to convert between.
Start the Conversion: Press the “Convert File” button to begin the process.
Download Your File: Once the conversion is complete, a download link for your new file will appear. Click it to save the file to your device.

Tip: If you see an error, your selected input format might not match your file’s actual format. Check the Troubleshooting Guide for help.

Understanding the Conversion Process

Converting between chemical formats is more than changing text; it involves interpreting and rebuilding the chemical structure.

The Input: A Universe of Formats

This tool supports over 100 file formats. Each format is designed for a specific purpose and stores different types of chemical information, such as:

1D Notations (smiles, inchi): The simplest way to represent a molecule’s atoms and bonds in a text string.
2D Connection Tables (mol, sdf): Store atom and bond lists, often used for chemical drawing software and storing libraries of compounds with associated data.
3D Coordinates (pdb, xyz, mol2): Store the (x, y, z) position of every atom in space, essential for molecular visualization, docking, and simulations.
Quantum & Molecular Mechanics Inputs (gjf, mopin): Highly structured files containing not just coordinates but also calculation settings like basis sets, charge, and multiplicity for specific simulation software.

The Core Transformation Process

Regardless of the formats involved, the converter performs these fundamental steps powered by Open Babel:

Parses the Input Format: It reads the input file according to the specific rules and syntax of the format you selected.
Builds an Internal Molecular Object: It creates a universal, in-memory representation of your molecule. This object contains all the atoms, bonds, coordinates, charges, and other properties read from the file.
Writes the Output Format: It takes the final molecular object and writes it to a new file, following the strict syntactical rules of your chosen output format. This step might involve losing data if the output format is simpler than the input (e.g., converting an sdf with metadata to a simple xyz coordinate file).

Troubleshooting Guide

General Tool Errors

Error: “File size exceeds the limit”
- Why it happens: Your uploaded file is larger than our server’s maximum allowed size (25 MB). This limit is in place to ensure fast and fair processing for all users.
- How to fix: For very large chemical library files (SDF) or complex macromolecular structures, consider splitting the file into smaller parts. For professional needs requiring the processing of larger files, please contact us to discuss custom solutions.
Error: “Processing timed out”
- Why it happens: The conversion for your molecule is taking too long. This can happen with extremely large or complex structures, or when performing computationally intensive operations.
- How to fix: Try to simplify your input file if possible. If the issue persists because your structure is inherently complex, please contact us to discuss options for handling larger computations.
Error: “CAPTCHA validation failed”
- Why it happens: Our system uses a CAPTCHA to prevent automated bots from overloading the server. This error occurs if the CAPTCHA was not solved correctly or timed out.
- How to fix: Simply reload the page and solve the new CAPTCHA challenge. If you continue to have trouble after reloading, please get in touch with our support team.

Conversion-Specific Errors

Error: “Could not read molecule or unrecognized format”
- Why it happens: The most common error. It occurs if the “Input Format” you selected in the dropdown does not match the actual format of your uploaded file, or if the file is structurally corrupt.
- How to fix: Double-check that you have selected the correct input format. For example, a PDB file needs pdb to be selected. Open the file in a text editor to ensure it isn’t empty or obviously corrupted.
Error: “Failed to generate 3D coordinates”
- Why it happens: You asked the tool to generate a 3D structure from a 1D or 2D input (like SMILES), but the algorithm failed. This can happen with very large molecules, molecules with ambiguous stereochemistry, or syntactically incorrect SMILES strings.
- How to fix: Verify your input SMILES or 2D structure is chemically correct. For very complex molecules, 3D coordinate generation can be difficult and may require specialized desktop software.
Warning: “Data was lost during conversion”
- Why it happens: This is not an error, but an important notice. It occurs when you convert from a feature-rich format (like sdf which can hold metadata) to a simpler one (like xyz which only holds coordinates). The simpler format cannot store the extra data, so it is discarded.
- How to fix: This is usually expected behavior. If you need to preserve all metadata, choose an output format that supports it, such as sdf or mol2.

Support Our Work

Your research matters, and we believe powerful scientific tools should be available to everyone, everywhere, without cost. This converter is built and maintained by a small team dedicated to open science. If this tool has helped you advance your project, please consider supporting our mission. Your contribution directly funds server maintenance, ongoing updates, and the development of new free utilities for the global scientific community. Can’t donate? You can still help! Sharing this tool with your colleagues and on social media is another powerful way to support our work. Thank you for being part of our community!

FAQ

How does this converter work?

This tool uses the Open Babel chemical toolbox, a world-class, open-source program, to function as its core engine. It scientifically interprets the structure, atoms, bonds, and coordinates from your input file, creates a universal internal representation of the molecule, and then writes that representation into the new file format you have selected, adhering to all of its specific rules and syntax.

Are my uploaded files stored on the server?

No. We take your privacy and data security extremely seriously. Your files are processed in memory for conversion and are permanently and irrecoverably deleted from our servers the moment the process is complete. We do not store or view any of your data.

Can I perform batch conversions?

The free web version of this tool is designed to process one file at a time. It is perfect for the day-to-day needs of most researchers. However, if you need high-throughput or batch processing of many files, please get in touch with our team through our contact page to discuss custom solutions.

References & Suggested Reading

O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33 The essential citation for the Open Babel project, detailing its architecture and capabilities. The source code is available on GitHub.

Meet the Authors

Mahdi Morshedi Yekta

Founder & Bioinformatics Developer

Mahdi is the founder of ScienceCodons and a Medical Biotechnologist with a deep passion for computational biology. Holding an M.Sc. in Medical Biotechnology, he specializes in transforming complex biological algorithms into accessible, high-performance web tools, bridging the gap between laboratory sciences and software engineering.

Fatemeh Faryadras

Medical Biotechnologist & Researcher

Fatemeh is a Medical Biotechnologist and researcher. With extensive expertise in genetic engineering, molecular cloning, and cancer biology, she combines her rigorous laboratory background with intuitive design principles to create reliable, user-centered scientific calculators and tools.

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