One of the most frequent challenges in molecular modeling is dealing with incompatible file formats. Whether you’re preparing a system for simulation, analyzing results, or sharing data with collaborators, you’ve likely faced the annoyance of having to convert files or losing data during import and export.
If you’re using SAMSON, this may be less of a problem than you think. SAMSON supports a wide range of formats—for molecular structures, trajectories, meshes, images, and more—making it easier to integrate workflows and share data without unnecessary friction.
Popular Formats for Molecular Structures
SAMSON reads and writes standard formats such as PDB, MOL2, SDF, and SMILES. For crystallographically relevant data, it also supports CIF and mmCIF (also referred to as PDBx). Trajectory data can be handled using formats like DCD, XTC, TRR, and NC (NetCDF).
Here’s a closer look at just some of the supported molecular structure file types:
- ARC – Tinker molecular and trajectory format
- CIF/mmCIF – Crystal structures or macromolecular data
- GRO, TOP, TPR – GROMACS structure and topology files
- LMPDAT – LAMMPS data support
- PDBQT – For AutoDock Vina docking (via SAMSON Extension)
Most of these formats can be both read and written directly by SAMSON. When a file format—like PDBQT or TPR—requires additional functionality for generation or parsing, SAMSON offers Extensions like the AutoDock Vina Extended or the GROMACS Wizard.
Flexible Embedding and Integration
SAMSON also goes beyond simple format compatibility. Its native SAM and SAMX formats are designed to hold comprehensive projects—including structures, meshes, notes, Python scripts, animations, and embedded files like PDFs and images. This lets you bundle your entire molecular project into a single file, which is helpful for ensuring reproducibility or sending a complete project to a colleague.
Trajectory File Support
If you’re working with simulation data, trajectory file management matters. SAMSON supports several trajectory formats, including:
- DCD – Binary trajectories from CHARMM, NAMD, or LAMMPS
- NC / NCTRAJ – AMBER NetCDF format
- TRR, XTC, TNG – GROMACS formats for high-performance and compressed trajectories
Thanks to the integration with the chemfiles library, you can use these trajectory types seamlessly, improving interoperability across toolkits and simulation engines.
No Support? No Problem
If SAMSON doesn’t yet support a format you need, you have two options: you can request support via the SAMSON Connect Forum, or you can write your own importers/exporters as SAMSON Extensions. The SAMSON SDK is designed to be extensible for exactly this kind of use case.
For a complete list of supported file types, and details about associated Extensions, refer to the full documentation on Supported Formats.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.