One of the most common—and often frustrating—challenges in molecular modeling is dealing with incompatible file formats. You’ve got simulations in LAMMPS, models from PDB, trajectories from GROMACS, and maybe some JSON-based DNA origami data for good measure. Ensuring that your molecular modeling platform can read and write all these different file types is essential to avoid redundant conversion steps and preserve data fidelity.
Thankfully, SAMSON, the integrative molecular design platform, supports an extensive range of file formats. Whether you’re importing a protein structure, analyzing a trajectory, or saving a visual mesh for 3D printing, SAMSON likely already supports the format you’re using.
Common Use Cases, Solved
🧬 Structures
SAMSON reads and writes many widely-used structural file types:
- PDB, mmCIF, and MMTF formats cover common protein and nucleic acid structures.
- MOL2, SDF, CML, and SMI help with small molecules, cheminformatics, and compound libraries.
- Formats like GRO, TOP, PSF, and LMPDAT are supported for users working with GROMACS, CHARMM/NAMD, and LAMMPS.
📊 Trajectories
Need to analyze a simulation result?
- XTC, TRR, TRJ, and TNG provide support for various GROMACS formats.
- DCD is available for CHARMM, NAMD, and LAMMPS users.
- NC/NetCDF trajectories are supported for AMBER workflows.
📐 3D Geometries
Exporting or importing 3D visuals or preparing meshes for 3D printing? SAMSON reads and writes OBJ and glTF formats and imports STL.
🖼️ Images and Movies
Capture your visuals by exporting in popular formats like PNG, JPG, BMP, and even create animations in GIF, MP4, or WEBM.
🧬 DNA Origami
If you’re working on DNA nanostructures, the Adenita extension supports ADN, ADNPART, JSON, and PLY formats commonly used in Cadnano and related software.
Flexible Scripting and Extensions
SAMSON also supports editing, executing, and saving .PY Python scripts directly within its built-in code editor. Advanced users can even extend support for additional formats by writing custom SAMSON Extensions for import and export workflows.
Explore the Full List
From .GRO to .STL, from crystallographic data to custom trajectories, SAMSON considerably reduces format compatibility headaches. If you’re dealing with data from a diverse stack of software, just open it in SAMSON—chances are, it’ll work out of the box.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it at https://www.samson-connect.net.