When working with molecular simulations, one of the most frequent causes of downstream issues is improperly prepared structural data. Whether you’re building coarse-grained models, simulating protein-ligand interactions, or setting up molecular dynamics runs, small inconsistencies in your input structures—like alternate locations, extra ions, or missing hydrogen atoms—can break workflows or lead to ambiguous outcomes.
SAMSON offers a guided process to help you clean up and prepare protein structures efficiently. In this post, we’ll walk through how to use the built-in preparation tools in SAMSON to make your atomistic models simulation-ready—especially when planning to generate coarse-grained (CG) models for the MARTINI force field.
Start From an Official Source
To keep things reproducible, begin by downloading a structure directly from the Protein Data Bank (PDB). You can do this directly within SAMSON by navigating to Home > Fetch. Enter the PDB code (e.g., 1UBQ for Ubiquitin) and select either the standard PDB format or the mmCIF representation.
Why Structural Cleanup Matters
Downloaded PDB structures often contain crystallization artifacts such as redundant water molecules, buffer ions, or incomplete side chains. These inconsistencies can cause issues later, especially in automatic topology generation tools like Martinize2. Cleaning the structure ensures molecule identification and renumbering work as expected.
SAMSON’s Protein Preparation Tool
Once your structure is loaded, head to Home menu > Prepare.
This action opens a panel that lets you effortlessly:
- Remove alternate locations for atoms
- Delete water molecules and ions
- Clean out ligands or small molecules used during crystallization
This step significantly simplifies the structural model, making it ready for techniques like CV modeling, docking, or CG transformation using Martinize2.
Tip
If your system includes biologically important water molecules or cofactors, double-check before deleting everything. You can deselect specific options in the cleaning interface.
Want to Dig Deeper?
If you’re curious about validating protein geometry, resolving missing atoms, and checking for chain gaps, SAMSON also provides a more detailed workflow: the Protein Preparation & Validation tutorial. It’s a good next step if you encounter more complex or incomplete structures.
Conclusion
Cleaning your structures before running simulations is a small step with big payoffs. With SAMSON’s streamlined tools, you don’t have to spend time manually curating PDB files. The GUI approach makes it accessible even if you’re not comfortable with scripts or command-line preprocessing tools.
Proper preparation is especially critical when working with topology-generation tools like Martinize2. If you work with coarse-grained modeling, be sure your input structure isn’t silently introducing issues that become evident only during simulation.
To learn more about creating CG models with Martinize2 in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net