If you’ve ever tried generating coarse-grained (CG) molecular models from multi-chain or multi-replica systems, you may have run into a frustrating issue: topology generation fails due to conflicting residue or chain IDs. This is a surprisingly common problem, and unfortunately, one that can be a roadblock when working with CG force fields like MARTINI in GROMACS. Fortunately, there’s a simple and effective solution built right into SAMSON.
Before running Martinize2 on a multi-chain structure or a system containing replicas of the same molecule, it’s essential to ensure unique identifiers for all residues and chains. If not handled properly, non-unique IDs can result in incorrect topologies, simulation errors, or unexpected behavior in your modeling workflow.
What needs to be renumbered?
In multi-protein systems (e.g., dimers, oligomers, or packed simulation boxes), each chain and residue must be uniquely identifiable. SAMSON helps you manage this by offering built-in tools to:
- Renumber residue IDs
- Renumber chain IDs
- Rename chains
How to renumber your model in SAMSON
Start by right-clicking on the structural model in your document (the top-level node in the Document view). Then, follow these steps:
1. Renumber Residue IDs
From the context menu, go to Structural model > Renumber residues and structural groups.
In the dialog that appears, leave the default start value (usually 1) and click OK.
2. Renumber Chain IDs
This ensures no two chains share the same ID.
Context menu: Structural model > Renumber chain IDs.
Again, leave the default value, then click OK.
3. Rename Chains
While unique numerical IDs are usually sufficient for generation, giving chains different names makes inspecting and editing models easier later on.
You can do this by selecting a chain, pressing F2 in the document view, or by right-clicking and selecting Rename.
Alternatively, use the Inspector for more controlled editing.
Why does this matter?
Martinize2 treats each structural model in SAMSON as an independent system. If chains or residues share identifiers across replicas or subunits, the topologies it produces might overlap, fail to compile under GROMACS, or lack the correct connectivity.
By renumbering and renaming, you avoid unintended coupling between chains and preserve the integrity of the CG system. It’s a small step that saves a lot of debugging down the line.
Conclusion
Renumbering chains and residues might feel like a detail, but it’s an essential part of building reliable coarse-grained molecular models—especially when working with multiple protein copies or assembling supramolecular complexes. If you’re seeing strange errors or topology mismatches, make sure unique chain and residue identifiers aren’t the culprit.
To learn more about preparing Coarse-Grained models in SAMSON using Martinize2, check the full tutorial at this documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.