When you’re working with molecular modeling software, one of the first real bottlenecks you might hit is file format compatibility. It often shows up when you try loading a structure you just downloaded from a public database—or even when trying to export your data into another tool for visualization, simulation, or presentation.
Unlike more monolithic modeling platforms, SAMSON offers extensive file format support that’s especially useful for scientists moving between tools like GROMACS, LAMMPS, AMBER, AutoDock, and more. This flexibility is one of the often underappreciated aspects of SAMSON that enables smooth, reproducible workflows across diverse toolchains.
Why does format support really matter?
If you’ve ever tried to load a trajectory file from one simulation tool into a visualization environment, you may have experienced the pain of cryptic errors or, worse, silent misinterpretations of your data. Each modeling or simulation software often has its own preferences for trajectory (*.trr, *.xtc, *.dcd), structure (*.pdb, *.mol2, *.gro), and topology (*.top, *.psf) files.
This is why knowing exactly what file formats an integrative platform accepts is critical. And especially when introducing a new tool like SAMSON into your workflow, it helps immensely to know not only what it can read, but also what it can write back when you export data for others. In other words, knowing format compatibility protects your time.
Highlights of File Format Compatibility in SAMSON
Here are some of the key integrations that stand out in SAMSON by format category:
1. Molecular Structures
- PDB, MOL2, SDF, CIF (mmCIF), PDBQT, SMILES — Opens the door to countless structure databases and computational docking tools.
- PSF, PRMTOP, PARM7, TOP — Useful for force-field-based simulations with CHARMM, NAMD, AMBER, and GROMACS.
2. Trajectories
- TRR, XTC, DCD, LAMMPSTRJ, NC/NetCDF — Covers most common trajectory formats used in major MD engines.
- SAMSON integrates with Chemfiles to organize and process molecular simulation outputs reliably.
3. Meshes and 3D Geometry
- OBJ, glTF, STL — Useful for exporting macromolecular surfaces or DNA origami designs into external 3D design tools or for 3D printing.
4. Embedded Formats
- Thanks to its own SAM and SAMX formats, SAMSON can not only store complex models and visualizations, but also embed scripts, notes, and folders into a single portable file.
5. Images & Animations
- Export static images into popular formats like PNG, JPG, BMP.
- Save viewport animations into GIF, MP4, WEBM to create illustrative videos for publications or presentations.
If you work across tools like Vina, GROMACS, Amber, CHARMM, LAMMPS, or just enjoy being able to transfer and transform your work freely, SAMSON’s extensive format support is designed to help you avoid unnecessary friction.
You can view the full list of supported formats in the SAMSON documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.