If you’ve ever tried to generate coarse-grained (CG) models for molecular dynamics simulations with multiple copies of the same protein, you’ve probably hit a frustrating problem: topology generation errors due to non-unique residue and chain identifiers. This issue is especially common when working with MARTINI force field using the Martinize2 tool in SAMSON. Fortunately, it’s simple to fix—if you know where to look.
This blog post walks you through how to resolve these issues by ensuring that residues and chains are uniquely identified when working with multiple replicas. We’ll use the example of the Ubiquitin protein (PDB ID: 1UBQ), but the approach is generally applicable. If you’ve ever received obscure errors after duplicating protein chains and trying to run Martinize2, read on.
Why this matters
When you duplicate chains to simulate multiple replicas (e.g., for membrane-protein systems or crowded environments), residues and chains might share the same numeric IDs and names. Tools that generate topologies, like Martinize2, rely on unique identifiers. Without them, they get confused—leading to inconsistent outputs or outright failure.
Instead of debugging file corruption or rewriting PDBs by hand, spend five minutes renumbering and renaming chains properly. Here’s how you do it in SAMSON.
Step-by-step: Renumbering and Renaming Chains
1. Renumber Residue IDs
In the SAMSON document view, right-click on the structural model (the top-level node), and choose:
Structural model > Renumber residues and structural groups
In the dialog, leave the default starting value at 1 and click OK.
2. Renumber Chain IDs
Next, right-click on the structural model again and go to:
Structural model > Renumber chain IDs
Leave the starting value at 0 and click OK.
3. Rename Chains by Name
Even if your chain IDs are unique, Martinize2 sometimes also relies on chain names. Rename them explicitly:
- Either select the chain in the document and press F2
- Or right-click and select Rename
- Alternatively, use the Inspector panel to rename chains
Best practices
- Renumber residue IDs before renumbering chains.
- Ensure all identifiers are unique across chains and residues.
- Save your SAMSON file after renumbering to prevent redoing this work.
Once this is completed, you can proceed to create CG models for each replica using Martinize2 without conflict. No more unexplained errors or misaligned topologies.
Learn more
For the full tutorial on using Martinize2 in SAMSON, visit the official 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.