A familiar frustration in molecular modeling: you receive a structure, a trajectory, and perhaps a topology file, but the extensions are unfamiliar—or the application opens one file while leaving you unsure what to do with the others. The first useful question is not simply “Can this file be opened?” It is “What kind of data does it contain, and do I need to read it, write it, or both?”
SAMSON supports formats for molecular structures, trajectories, 3D geometry, images, scripts, and more. Here is a practical way to use its format list to plan a workflow and avoid common file-format surprises.
Start with the data you have
A molecular structure describes a molecular system. Common examples listed for SAMSON include PDB, mmCIF (also called PDBx), SDF, MOL2, GRO, and XYZ. If you need a format that can both be opened and saved, check the Read and Write columns for that specific format. Support is not always symmetrical: for example, MMTF is listed for reading, but not writing.
A molecular trajectory contains coordinate frames over time. SAMSON lists formats including DCD, AMBER NetCDF (NC), TRR, XTC, PDB, and XYZ. Some formats in the list are read-only—for example, TNG and TRJ—while DCD, NC, TRR, and XTC are listed for both reading and writing. That distinction matters if your plan includes exporting after analysis.
A topology or structure companion file may also be part of the job. The documentation specifically notes that AMBER topology files, with extensions such as PARM7 or PRMTOP, are used when loading AMBER NetCDF trajectories. So if your trajectory is an AMBER .nc file, keep its topology file available rather than treating the trajectory as the only input.
Read the table as a workflow check
Before moving files between tools, check three things:
- Identify the data type. Is the file a structure, a trajectory, a mesh, or something else? A file extension alone may not tell you how it will appear in the application.
- Confirm the direction. “Read” means SAMSON can import that format; “Write” means it can export it. A blank cell does not indicate support in that direction. Some formats also depend on an extension, as noted in the documentation.
- Keep related files together. When the format requires a companion file—as the documentation describes for AMBER NetCDF and its topology—include both when preparing the data.
This small check can prevent a common workflow detour: discovering only at the export stage that the chosen format is not writable, or realizing that a trajectory needs additional input. If you are preparing a handoff to a colleague, it is also useful to state which files are structures, which are trajectories, and which are supporting topology files.
When the format is not listed
The supported-formats page is explicitly non-comprehensive, and SAMSON Extensions may support additional formats. Some listed formats are associated with particular extensions: for example, the GROMACS Wizard can generate GROMACS project files, while AutoDock Vina Extended can generate PDBQT files and load PDBQT files from its docking projects. Check the relevant extension details before assuming a format is available in a default installation.
If a format you need is not supported, the documentation suggests contacting the SAMSON Connect Forum or developing an importer or exporter. For a complete list of formats and their read/write support, see the supported-formats documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.