When working with protein systems that include multiple replicas—either for crowding simulations, protein-protein interaction analysis, or other ensemble-based studies—generating coarse-grained (CG) models using the MARTINI force field can be challenging if your atoms, chains, or residues aren’t uniquely identified. One common but preventable issue is structure clash or incorrect topology generation during conversion from atomistic to CG models.
To help you with this, the Martinize2 Extension in SAMSON provides built-in tools to renumber chains and residues—a crucial step before coarse-graining multi-chain or multi-replica protein systems.
Why Renumbering Matters
GROMACS and topology generators like Martinize2 expect each residue and each chain to have a unique identifier. If multiple chains share the same residue or chain IDs, the result can be ambiguous topologies or simulation errors. This is especially important when modeling crowding environments or multimeric complexes.
Step-by-Step: Ensuring Unique Residue and Chain IDs
Let’s go through how SAMSON helps avoid these issues with a simple sequence:
- Renumber Residue IDs: In your SAMSON project, right-click the structural model. From the context menu, choose:
Structural model > Renumber residues and structural groups.
In the dialog that appears, leave the start value as 1 and click OK.
- Renumber Chain IDs: Again, right-click the same structural model and choose:
Structural model > Renumber chain IDs.
Leave the start ID as 0 and click OK.
- Rename Chains: Unique names make tracking chains easier, especially in complex systems. You can click a chain in the Document and press F2 to rename, or right-click and select Rename.
For more advanced batch editing, the Inspector is also handy:
Tips for Larger Systems
- Chain and residue renumbering can be scripted using SAMSON’s Python API for automation.
- Make sure to save your structure after renumbering to avoid starting over.
- This cleanup step is best done before using Martinize2 to avoid redoing model generation.
What If You Skip This?
Skipping renumbering might work for single-chain systems but will almost certainly cause problems in multi-replica setups. You could end up with overlapping residues in a combined topology or cryptic simulation crashes.
If you’re running into errors that don’t make sense during topology generation—even if Martinize2 doesn’t report anything specific—checking that all residues and chains are uniquely identified should be one of your first moves.
To explore the full documentation and learn how to create CG models using Martinize2 from start to finish, visit the Martinize2 tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net.