Avoid Topology Errors: How to Renumber Chains and Residues in Replicated Protein Systems

If you’ve ever tried to simulate a system with multiple replicas of the same protein and ran into topology generation errors, you’re not alone. This is a common issue when working with coarse-grained modeling tools like Martinize2 in SAMSON. The good news is there’s a straightforward solution — and it’s often just a matter of properly renumbering chains and residues.

This post outlines how to correctly prepare replicated proteins for MARTINI coarse-graining using SAMSON’s Martinize2 extension by ensuring each chain and residue gets a unique identifier. This step can prevent frustrating errors later in the simulation workflow and streamline your structure setup.

Why Renumbering Matters

When creating multiple replicas of a protein (for example, by manually duplicating protein chains to build up a molecular box), the newly created chains often retain the same chain IDs and residue numbering as the original. Martinize2 requires all residues and chains to have unique identifiers to generate valid topology files.

Without unique residue IDs or chain names, Martinize2 may either fail silently or produce incorrect topologies — leading to incorrect results or simulation crashes.

Step-by-Step: Renumbering Chains and Residues

Once you’ve created your protein replicas (manually or using scripts or tools like the Molecular Box Builder), follow these steps inside SAMSON:

1. Renumber Residue IDs

Right-click on the structural model in the document and navigate to:

In the dialog that pops up, leave the default starting value at 1 and click OK.

2. Renumber Chain IDs

Right-click again on the structural model and go to:

In the dialog, leave the starting ID at 0 and click OK.

3. Rename Chains for Clarity

Even after assigning unique IDs, it’s a good idea to rename your chains so their identities are easier to interpret. You can do this in two ways:

• Directly in the document view: select a chain and press F2, then type a new name.
• Using the Inspector: select the chain, and modify its name in the Inspector panel.

Once these steps are completed, your system is ready for coarse-graining with Martinize2, and each replica will be treated correctly without naming conflicts.

Pro Tip

Don’t forget to save your project once renumbering is complete. This way, you can return to your correctly prepped system without repeating these steps.

Conclusion

Renumbering might seem like a minor detail, but skipping it can lead to major issues downstream. Whether you’re modeling membrane systems, crowded environments, or dense protein solutions, making sure your replicas are uniquely identified is essential for reproducible and accurate simulations.

For a complete walk-through on creating coarse-grained models with Martinize2 in SAMSON, check out the official documentation: 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.