Opening Your Favorite Molecular Formats in SAMSON

Working with collaborators or datasets from different software tools often means dealing with a variety of molecular file formats. If you’ve ever tried to view or edit a specific file in your molecular modeling platform only to realize it’s not supported, you’re not alone.

SAMSON, the integrative molecular design platform, offers wide-ranging support for molecular structure and trajectory file types — and knowing this can save researchers real time.

Why this matters

Molecular researchers often deal with structures from many sources: quantum chemistry outputs, crystal structure databases, or docking results. Formats like PDB, SDF, MOL2, or XYZ are common, but others like GRO and DCD are essential in simulation workflows. Lack of support for even one can slow down work or force format conversion.

SAMSON simplifies this by supporting many file types directly, and through extensions adds even broader compatibility.

Supported molecular structure formats

SAMSON comes with built-in support for popular molecular structure formats such as:

  • PDB (also aliases like ENT, VDB): often used for protein and nucleic acid structures.
  • SDF, MOL2, and SMI: common in drug discovery and cheminformatics.
  • CIF and mmCIF: crystallographic information files, with support enhanced by the Crystal Creator extension.
  • XYZ: simple coordinate trajectory format, useful for quick visualization or scripting.
  • LMP, LMPDAT: LAMMPS data files, including aliases like DATA.

These formats retain important molecular information such as atom types, coordinates, topology, and bonding. In SAMSON, you can visualize, edit, and save them without additional conversions.

Trajectory formats for simulations

For those running simulations in engines like GROMACS, AMBER, or LAMMPS, SAMSON supports commonly used trajectory formats such as:

  • DCD: standard for CHARMM and NAMD users.
  • NC: AMBER’s NetCDF trajectory format.
  • XTC, TRR, TNG: compressed and uncompressed trajectory outputs from GROMACS.

This means you can view and analyze molecular motions directly in SAMSON, overlaying them with structures or visualizations.

Extending support with SAMSON Extensions

Have a file that’s not opening? In many cases, installing a SAMSON Extension adds new file compatibility. For example:

  • AutoDock Vina Extended adds support for reading and writing PDBQT files used in docking workflows.
  • GROMACS Wizard helps generate TPR, TOP and other GROMACS project files.
  • SMILES Manager expands how SMILES strings are imported/exported (SMI).

SAMSON makes it easy to discover these extensions directly through SAMSON Connect.

Added flexibility with embedding

Beyond dedicated formats, SAMSON can embed nearly any kind of file into a document – whether it’s Python scripts, images, or associated data. This ensures that users can package all relevant information together for collaboration or archiving.

Conclusion

Knowing which formats your platform supports can make cross-tool workflows far smoother. Whether you’re importing a result from another group or saving simulations to analyze in another program, SAMSON has you covered with a surprisingly wide range of import/export options.

→ View the full list of supported formats in the SAMSON documentation

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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