If you’ve ever tried to import a structure file into one tool, only to export it for another, you know the pain: data loss, conversion issues, and a lot of time spent trying to figure out which formats are supported. Whether you’re dealing with small molecules or entire protein complexes, navigating molecular file formats can be a challenge.
That’s where SAMSON comes in, offering robust support for a broad set of file formats used in molecular modeling. This post explores the range of file types supported by SAMSON, specifically focusing on molecular structure formats—one of the most important data types for researchers, educators, and students working in computational chemistry, biology, and nanoscience.
Why file format support matters
When working on molecular projects, you often combine tools: maybe you’re conducting a simulation in GROMACS, interpreting results in VMD, or preparing structures in Chimera. Each tool has its own preferred input and output formats. You need flexibility—especially when collaborating across research groups or disciplines.
SAMSON helps by supporting over 20 widely-used molecular structure file types, and enabling additional format support through extensions. Let’s look at how SAMSON handles some of the most common formats in molecular modeling.
Common formats supported
- PDB & mmCIF: The go-to for protein structures, both standard PDB and PDBx/mmCIF (macromolecular CIF) files are fully supported.
- SDF, MOL2, SMILES: Whether you’re working in cheminformatics or importing ligands, you can use these formats for small molecules.
- LAMMPS (DATA, LMP, LMPDAT): If you use LAMMPS for simulation, you can import and export its data file structure with ease.
- GROMACS (GRO, TOP, TPR): SAMSON can open structure and topology files and even write topology data with additional extensions.
- Others: ARC (Tinker), CIF (crystal structures), CML, PSF, MMTF, XYZ — the list goes on.
Write and read support
Not only can SAMSON read these formats, it can also write back to most of them. For example, SDF, PDB, MOL2, and XYZ can be both read and written, allowing round-trip editing. This is crucial for workflows where you build or edit molecules in SAMSON and need to use them elsewhere.
SMILES and extensions
SMILES strings are increasingly used because of their compact representation of molecules. SAMSON supports reading and writing SMILES directly, and its SMILES Manager extension allows importing and generating SMILES from structures, streamlining this part of the workflow.
Don’t see your format?
SAMSON is also extensible. If the format you’re using isn’t supported out of the box, you or your team can develop importers/exporters. Or, check the Extension Store—SAMSON Extensions frequently add support for niche or domain-specific formats.
Conclusion
File format compatibility should never be the hurdle that slows down your research. With native support for a wide selection of molecular structure formats—and the ability to expand this set via extensions—SAMSON can simplify your workday by integrating more of your data into a single workspace.
Learn more about all supported formats and how to work with them in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.