One frequent hurdle for molecular modelers is dealing with multiple file formats across different simulation platforms. Whether you’re copying data between tools or collaborating across research groups, compatibility becomes a constant worry. You’ve likely asked yourself: "Will this software load my simulation? Does it export the format my team needs?"
If you’re using SAMSON—the integrative molecular design platform—you may be surprised at how many formats it supports right out of the box for importing and exporting molecular systems, trajectories, 3D geometries, scripts, and more. And when support is missing, there’s often an extension already available—or you can build your own.
Supported file types in SAMSON
Molecular structures: SAMSON can work with a wide range of structure formats including mainstream standards like PDB, CIF, MOL2, and SDF—but also with specialized ones such as ARC (Tinker) or LMP (LAMMPS data). Formats such as XYZ and SMILES are also supported, making it convenient for users working with simple geometries or cheminformatics tools. Of note, CIF support covers both crystalline and macromolecular data (mmCIF/PDBx).
Molecular trajectories: SAMSON supports file types used in major molecular dynamics packages such as:
DCD– CHARMM, NAMDXTC,TRR– GROMACSNC/NCDF– AMBER NetCDFLAMMPSTRJ– ASCII trajectories from LAMMPS
These formats are readable and in many cases writable, allowing you to load simulation data and save processed results.
3D geometries: If you want to save surface meshes or visual models as 3D objects, SAMSON supports exporting to OBJ and glTF. These can be read and written, making it possible to use SAMSON in visualization pipelines or integrate physical molecular models via 3D printing workflows.
Python scripts: For developers and researchers scripting simulations or visualizations, SAMSON accepts *.py files. You can read, write, and execute Python files using the platform’s built-in Code Editor, which is helpful for those embedding custom logic inside workflows.
Images and animations: SAMSON can capture scenes directly to standard image formats such as PNG, JPG, BMP, and even export movies in MP4 and WEBM formats. GIF is supported too—useful for simple looping animations.
Extensions unlock even more formats
Some specialized formats are enabled through extensions. For example:
- AutoDock Vina Extended adds support for
PDBQTfiles, used in molecular docking. - GROMACS Wizard lets you generate and interpret
TOPandTPRfiles. - Adenita adds formats for DNA origami such as
ADN,ADNPART, andPLY.
If a format you need is still missing, SAMSON even supports building your own importer/exporter through its extension system. You’ll find guidance for this in the Importers and Exporters sections of their guides.
So whether you’re bringing in molecular data from a crystallographic database, working on a GROMACS simulation, preparing input for a docking run in AutoDock, or exporting meshes for 3D printing—chances are, SAMSON can handle the format you need.
Learn more in the full documentation →
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.