If you’ve ever tried to work with molecular structures from a variety of sources, you’ve likely faced the challenge of incompatible file formats. Maybe you received data from a collaborator in a format your tool doesn’t recognize. Or perhaps you found an interesting molecule online but couldn’t load it into your modeling software. If that sounds familiar, this post is for you.
SAMSON is an integrative platform for molecular design that supports a wide range of file types, making it easier to bridge gaps between file formats from different tools and ecosystems. Let’s take a closer look at what formats you can import and export when working with molecular structures in SAMSON.
🧬 Overview of Supported Molecular Structure Formats
Here are some of the commonly used formats supported for both reading (import) and writing (export):
- PDB – the standard Protein Data Bank format. SAMSON supports a variety of aliases such as ENT, VDB, PDB1, PDB2, etc.
- CIF / mmCIF – for crystallographic data. You can even use the Crystal Creator App to handle CIF files.
- SDF / MOL – chemical table formats that are widely used in cheminformatics.
- SMI (SMILES) – linear notations for molecules, readable and writable directly or through the SMILES Manager.
- MOL2 – Tripos MOL2 format for comprehensive molecular definitions.
- LMP, LMPDAT – LAMMPS data files (aliases: DATA).
- GRO, TOP, TPR – GROMACS formats, compatible through the GROMACS Wizard extension.
- PDBQT – used in docking; handled via AutoDock Vina Extended.
📌 Format Aliases and Compatibility Notes
One friendly feature of SAMSON is alias support. For example, PDB files may use different extensions, like .pdb1 or .ent—SAMSON can recognize these. This can save time and avoid manual renaming.
Moreover, SAMSON doesn’t stop at structural formats. It also supports formats for:
- Molecular trajectories like DCD, TRR, XTC, NC, ARC, and more
- 3D geometries, such as OBJ and glTF, which are useful for visualizing meshes
- Images and animations: BMP, PNG, GIF, MP4, etc.
🔁 Extensions for Even More Format Support
In some cases, certain file types are supported through SAMSON Extensions. These are modules you can install directly from SAMSON Connect. Extensions like the AutoDock Vina Extended and GROMACS Wizard not only provide compatibility but allow users to read, write, and visualize results from external tools seamlessly inside SAMSON.
For example, while SAMSON supports the PDBQT format, it must be used with the AutoDock Vina Extended extension. Similarly, TOP and TPR files can be handled through the GROMACS Wizard. This modularity keeps the platform lightweight but expandable depending on your needs.
📂 Exporting and Sharing Your Work
Writing files (exports) is straightforward—SAMSON supports exporting to nearly every format it can read. This includes SDF, MOL2, CIF/mmCIF, SMILES, XYZ, and even GROMACS input formats. If you work in multi-tool environments, this is especially helpful for seamless handovers and compatibility.
To view the complete and detailed format compatibility list, including molecular trajectories, 3D meshes, and images, refer to the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.