A molecular file can be perfectly valid and still be the wrong file for the next step in your workflow. Perhaps a structure loads, but you are unsure whether it can be exported again. Or you have a trajectory without knowing which topology file belongs with it. These small compatibility uncertainties can cost time—especially when a format name is used for more than one kind of data.
A useful first step is to separate three questions: What kind of data is this? Can SAMSON read it? And can SAMSON write it? The supported-formats reference answers the last two separately. A listed format may be readable, writable, or both; do not assume that opening a file means the same format is available for export.
Start with the data, not just the extension
Extensions can appear in more than one category. For example, PDB is listed for both molecular structures and molecular trajectories, with read and write support in each category. XYZ also appears in both: it is listed as readable and writable for molecular structures, but only readable for trajectories. So if a file ends in .xyz, its role in your project matters as much as its suffix.
This distinction is especially helpful when planning a conversion. If you intend to export a trajectory, check the Molecular trajectories section—not only the molecular-structure table. There, formats such as DCD, NC, TRR, and XTC are listed as both readable and writable. Other trajectory formats, including TNG, TRJ, and LAMMPSTRJ, are listed for reading, with no write support shown.
Check companion files before loading a trajectory
Some trajectory workflows involve more than one file. The format reference notes that PARM7 and PRMTOP are AMBER topology files used when loading AMBER NetCDF trajectories. That is a useful reminder to identify the associated topology as well as the trajectory itself. If a trajectory does not look as expected, checking whether you selected the appropriate companion file is a sensible troubleshooting step.
Likewise, distinguish a structure or topology from a simulation trajectory. The GROMACS TPR format is described as a run topology file, while TRR and XTC are trajectory formats. The reference lists TPR and TOP as readable, and notes that writing them is handled by the GROMACS Wizard extension. That distinction can help you choose the right input and set realistic expectations for export.
Look for extension-specific formats
Some workflows depend on a SAMSON Extension rather than the built-in format support alone. For instance, the documentation associates PDBQT reading and writing with AutoDock Vina Extended, which can also load PDBQT files from docking projects created using that extension. The CIF entry also points to the Crystal Creator App for crystal structures. When a table includes an extension note, treat it as part of the workflow checklist: confirm that the relevant extension is available before relying on that capability.
A quick pre-conversion checklist
- Identify the data type: structure, trajectory, mesh, image, or another kind of file.
- Check both directions: confirm read and write support separately for the specific category.
- Find companion inputs: for example, an AMBER topology file when working with an AMBER NetCDF trajectory.
- Check extension notes: some formats or exports depend on a named extension.
- Verify the result: after export, reopen the output or otherwise check that it contains the data you intended to transfer.
This small check can prevent a common workflow surprise: discovering only at the end that a format is supported for import but not for the export you need. The full SAMSON supported-formats reference covers molecular structures, trajectories, 3D geometries, images, animations, DNA origami, and more.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.