A model can look perfect in one molecular tool and become a frustrating puzzle in another: the file may open, but the receiving application may need a different format, a matching topology, or an extension to handle it. Before exporting, it helps to ask two simple questions: What kind of data is this file carrying? and Does SAMSON read it, write it, or both?
SAMSON supports many molecular structure and trajectory formats, but support is not identical in both directions. A format listed as readable is not automatically writable, and a writable format may require an extension. Checking that distinction first can save a round trip through an unsuitable file type.
Start with the data you need to move
For a molecular structure, the documented options include PDB, SDF, MOL2, XYZ, GRO, and others. PDB and SDF, for example, are listed for both reading and writing. CIF is readable, and can be written in PDBx/mmCIF format. Other formats have more limited support: MMTF, PSF, and AMBER topology files are listed as readable, with no write support shown on this page.
That distinction matters when planning a handoff. If a collaborator requests a format that SAMSON can read but not write, importing their file is only half the workflow. Check the destination format before you start editing, and choose a supported export route that suits the next step.
Keep trajectory and topology files together
Trajectory files are not the same as standalone structures: they contain changing coordinates over time. SAMSON lists formats such as DCD, AMBER NetCDF (NC), PDB, TRR, XTC, and XYZ for trajectory reading and writing. Other trajectory formats in the list are read-only. For instance, TNG and LAMMPSTRJ are listed for reading, but not writing.
When moving a simulation to another program, identify the files that describe the coordinates and the files that describe the system. Some trajectory workflows depend on an associated structure or topology file. The documentation specifically notes that AMBER topology files can be used when loading AMBER NetCDF trajectories. Keeping related files together and recording which topology belongs with which trajectory makes a handoff easier to reproduce.
Check whether an extension is needed
Some formats rely on SAMSON Extensions. PDBQT support is associated with AutoDock Vina Extended, which can also load PDBQT files from its docking projects. GROMACS project files such as TOP and TPR can be generated with GROMACS Wizard. The SMILES Manager extension can read and generate SMILES. The supported-formats reference identifies these extension-specific cases, so check it before assuming a format is available in the base installation.
Choose the right kind of SAMSON file
If your goal is to save a working SAMSON document rather than exchange only molecular coordinates, consider SAM or SAMX. These native formats support a broad 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 for keeping a project and its supporting materials together. For exchange with another application, use a format that the other application accepts instead.
A quick pre-export checklist
- Identify the content: structure, trajectory, mesh, image, or full SAMSON document.
- Check both directions: confirm whether the intended format is supported for reading, writing, or both.
- Look for extension notes: formats such as PDBQT and GROMACS project files may require a specific extension.
- Keep related files together: especially when a trajectory is used with a topology or structure.
- Verify the result: reopen the exported file or check it in the receiving application before relying on the handoff.
These checks are especially useful when exchanging work across molecular modeling, simulation, and visualization tools: the filename extension alone does not tell you whether the needed data can be imported or exported. For the complete, non-exhaustive list of formats and their read/write support, see the SAMSON supported formats reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.