Few things interrupt a modeling workflow like discovering that a file can be opened in one tool but not saved in the format your next step expects. The extension on a filename is a useful clue, but it does not tell the whole story: a format may be supported for reading, writing, or both, and some workflows depend on an additional extension.
This guide helps you check those details before you start converting files in SAMSON. The aim is simple: choose a practical route for moving structures, trajectories, and project data without assuming that every format works in both directions.
Start with the direction of travel
When checking a format, ask two separate questions: can SAMSON read it, and can SAMSON write it? The supported-formats reference lists these capabilities independently. A format with a read mark but no write mark may be suitable for bringing data into a project, but it is not listed as an export option. For example, MMTF and Molden are listed for reading molecular structures, while the molecular-structure table does not list them for writing. Conversely, SAM and SAMX are listed for both reading and writing.
This distinction matters when planning a handoff. If you need a file that another application can consume, check the write column for the specific format you intend to use—not just whether SAMSON can open that file type.
Choose between a working project and an exchange file
For work you want to keep in SAMSON, consider its native SAM and SAMX formats. The documentation describes these as supporting a wide range of SAMSON data, including molecular structures, groups, visual models, meshes, animations, notes, and simulators. They can also embed folders and files such as scripts, PDFs, images, and other data. That makes them useful when the goal is to keep a richer project together, rather than simply pass a molecular structure to another tool.
For exchanging molecular structures, the listed options include familiar formats such as PDB, SDF, MOL2, GRO, and XYZ, among others. Their capabilities differ, so check the table before settling on one. For instance, PDB and SDF are listed for reading and writing, while PSF is listed for reading. CIF is listed for reading and writing in PDBx/mmCIF format. These distinctions can help you avoid a last-minute export problem.
Keep trajectory files in their own category
A trajectory is not the same thing as a structure file. SAMSON’s reference lists trajectory formats separately, including DCD, AMBER NetCDF (NC), TRR, XTC, and XYZ. Some are listed for both reading and writing, while others—such as TNG and LAMMPSTRJ—are listed for reading. If your task involves a simulation trajectory, use that section rather than assuming that the structure-format entry for the same extension tells you everything.
One important workflow detail is called out for AMBER NetCDF trajectories: the PARM7 or PRMTOP topology file is used when loading them. Keeping the topology and trajectory files together makes it easier to identify the files belonging to the same dataset when you prepare to load them.
Check whether an extension is part of the workflow
Not every listed capability is available in the same way. PDBQT support is associated with the AutoDock Vina Extended extension, which can load PDBQT files from docking projects and generate PDBQT files. GROMACS project files can be generated with the GROMACS Wizard extension. DNA-origami formats in the reference are supported by Adenita.
A quick preflight check can save time: identify whether you need to import or export; confirm the relevant table entry; note any extension requirement; and, for trajectories, check whether a companion topology file is mentioned. Also remember that the reference describes itself as non-comprehensive: SAMSON Extensions may support additional formats that are not listed.
For the full tables and format-specific notes, see the SAMSON supported formats documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.