Choosing the right platform for molecular modeling can depend heavily on its ability to handle the variety of file formats researchers use daily. For molecular modelers working across simulation packages, crystallography tools, and cheminformatics platforms, file compatibility often becomes a bottleneck. Translating between different formats, worrying about data loss during conversion, or simply not being able to open a file are all hurdles that slow down scientific workflows.
SAMSON, the integrative molecular design platform, addresses this challenge by supporting a wide range of molecular file formats—making it easier to move from visualization to simulation, data analysis, and beyond, without switching tools or fighting with converters.
Supported Molecular Structure Formats
SAMSON supports many of the most commonly used file formats to read and write molecular structures. This makes it easy to import structures from other software or databases and export results for sharing or further analysis elsewhere.
- PDB / mmCIF / MMTF — Widely-used formats for macromolecular structures.
- MOL2 / SDF / CML / SMILES — Popular in cheminformatics and virtual screening.
- GROMACS files (.GRO, .TOP, .TPR) — Read and write support allows for seamless integration with GROMACS workflows.
- AMBER files (.PRMTOP, .NC, .PARM7) — Used in combination with trajectory formats like NetCDF.
- LAMMPS Data (.LMP, .LMPDAT, .LAMMPSTRJ) — Enable modeling setups across platforms.
SAMSON even supports formats like XYZ and CSSR, offering interoperability with tools like Tinker and Molden.
Trajectories and Dynamic Systems
For users working with molecular dynamics, SAMSON provides read and write support for trajectories in the following formats:
- DCD – CHARMM, NAMD, and LAMMPS binary trajectories.
- TRR / XTC / TNG – GROMACS-specific trajectory formats.
- NC / NetCDF – Used in AMBER simulations.
This compatibility means you can not only view but also process and analyze trajectories generated from various molecular dynamics engines, all within one environment.
What About 3D and Visualization Data?
Molecular modelers often need to convert structures into visual formats for presentations or printing. SAMSON lets users export models as 3D geometries, including:
- OBJ – Wavefront format, great for 3D printing and rendering.
- glTF – Web-friendly format allowing interactive 3D on the web.
Working With Python
SAMSON can read, write, and execute .py files directly thanks to its built-in code editor. This is useful for users integrating scripting workflows in modeling, automation, or custom analysis routines.
Need More?
Despite the broad native support, even more formats can be handled through SAMSON Extensions. For example:
- AutoDock Vina Extended makes it possible to handle PDBQT files.
- GROMACS Wizard can generate compatible GROMACS topology files.
- Adenita supports DNA origami designers with ADN, ADNPART, and Cadnano JSON formats.
These extensions are lightweight and free to install, maintaining the flexibility of SAMSON without overloading its core.
If a particular format isn’t supported yet, users can even create their own importers and exporters using SAMSON’s documented API.
Learn more in the detailed documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.