Working with systems that involve multiple copies of the same protein is increasingly common in coarse-grained molecular dynamics simulations — especially when simulating crowded environments or modeling self-assembly. Tools like Martinize2 help generate coarse-grained (CG) topologies for the MARTINI force field, but creating reliable CG models for replicated protein systems comes with its own challenges. A typical and frustrating issue: your simulation fails because residues or chains are not uniquely identified across replicas.
If you’ve run into topology generation errors or strange behavior due to multiple chains having identical names, this walkthrough should save you time and confusion. We’ll show you how to correctly set up and number your replicas in SAMSON before passing them to Martinize2.
Why Unique Chain & Residue IDs Matter
Martinize2 treats each top-level structure (called a “structural model” in SAMSON) as a separate input model. But if your system contains multiple chains or residues with the same IDs or names, the generated topology files can end up with conflicts that prevent simulations from running properly in GROMACS.
This is especially true when manually duplicating proteins inside the same structural model or using a builder tool.
Renumbering and Renaming Steps
Once you’ve duplicated your protein replicas (via copy-paste or using tools like the Molecular Box Builder), follow these three steps to make your system simulation-ready.
1. Renumber Residue IDs
Right-click on the structural model and navigate to Structural model > Renumber residues and structural groups.
In the dialog that opens, start at 1 (the default) to give unique, sequential IDs to all residues.
2. Renumber Chain IDs
Right-click on the structural model again and choose Structural model > Renumber chain IDs.
Use the default starting point (typically 0) to ensure each chain in your system gets a unique ID.
3. Rename Chains
You can rename chains manually to make the document more readable and avoid naming duplicates. Select a chain, press F2, or right-click and choose Rename.
Alternatively, use the Inspector to manage chain names more interactively:
Save Before You Proceed
After cleaning up your chains and residues, save the system to a file. It’s a simple step that helps you avoid redoing work if something unexpected happens during CG model generation.
From Here, Continue the CG Modeling Workflow
Now that your structural model is clean and properly formatted, you can proceed to use Martinize2 as usual: set up your force field options, define restraints if needed, and generate the CG structure and topologies.
By ensuring unique identifiers at the chain and residue level, you’ll ensure cleaner outputs and minimize the risk of simulation setup issues later on.
🔗 Learn more in the full Martinize2 tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.