A molecular trajectory can be perfectly valid and still be the wrong file to open on its own. When a simulation will not load—or when you need to move data between tools—the first useful question is not just “What is the extension?” It is “What kind of data is this file, and can SAMSON read or write it?”
This quick guide uses the supported-format list to help you check that before spending time troubleshooting. It focuses on molecular structures and trajectories, where formats can serve different roles even when they come from the same simulation workflow.
First, separate a structure from a trajectory
A structure file describes molecular coordinates and related structural information. A trajectory represents coordinates across a series of frames. The supported-format reference lists these categories separately, which is a helpful reminder: two files from one project may need different handling.
For example, SAMSON lists PARM7/PRMTOP as an AMBER topology file used when loading AMBER NetCDF trajectories. The trajectory itself is listed under NC, with NCDF and NCTRAJ as read aliases. In other words, identify both the trajectory and any associated topology file your workflow requires; do not assume the trajectory extension alone tells the whole story.
Use the Read and Write columns as a compatibility check
The format list marks whether SAMSON can read and write each listed type. A blank cell is important: it means the documentation does not list that operation as supported for that format. Read support does not automatically mean write support.
- DCD: listed for reading and writing; described as a CHARMM, NAMD, or LAMMPS binary trajectory.
- NC: listed for reading and writing; the AMBER NetCDF trajectory format.
- TRR: listed for reading and writing as a GROMACS trajectory.
- XTC: listed for reading and writing as a compressed GROMACS trajectory.
- ARC: listed for reading, with no write support shown in the trajectory table.
- TNG, TRJ, LAMMPSTRJ, and XYZ: listed for reading, with no write support shown there.
This check is especially useful when planning an export. If you need to produce a file for another program, confirm that the specific format is listed as writable rather than choosing based on familiarity or file extension alone.
Check the structure format separately
SAMSON lists several common molecular structure formats, including PDB, SDF, MOL2, GRO, and XYZ. Many are shown as both readable and writable, but not all formats have the same capabilities. For instance, MMTF and MOLDEN are listed for reading, while PSF and PARM7/PRMTOP are also listed as read-only in the structure table.
Some formats also have aliases. PDB can be read using aliases such as ENT and VDB; SDF has MOL and SD read aliases; and LMP/LMPDAT has DATA as a read alias. If a file is not recognized by its expected extension, the alias information may help explain why—but it is still worth confirming what the file contains.
Account for extension-dependent formats
Not every listed capability is available by default. The documentation notes that some formats require a SAMSON Extension. For example, PDBQT support is associated with AutoDock Vina Extended, while GROMACS project-file generation is associated with GROMACS Wizard. DNA origami formats are supported by Adenita. If a format appears in the reference but is unavailable in your installation, check the extension named alongside it.
A simple preflight checklist
- Decide whether you are opening a molecular structure or a trajectory.
- Identify any companion topology file needed by your simulation format.
- Look up the exact format and aliases in the supported-format reference.
- Check the Read and Write columns for the operation you need.
- Check whether the listed support depends on an extension.
This small check can save time when moving molecular data between tools: it helps distinguish an unsupported export from a missing extension, and a trajectory from the structural information it may depend on. For the full list of categories, formats, aliases, and extension notes, see the SAMSON supported formats reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.