When working with coarse-grained (CG) molecular models, it’s common to simulate multiple copies—or replicas—of the same protein in a single system. This setup is especially useful for studies involving protein aggregation, diffusion, or encapsulation. However, many researchers new to coarse-graining run into a frustrating issue: chain and residue conflicts during topology generation.
If you’ve ever tried to generate a CG model using Martinize2 and encountered warnings or errors about duplicate chain names or overlapping residue IDs, you’re not alone. The source of the problem is often simple: when copying chains to create replicas, chain names and residue numbers frequently remain identical. Most topology builders—including Martinize2—expect these to be unique so they can keep track of which atoms (or beads) belong where.
Replicas Without the Headache
The good news is that SAMSON, the integrative molecular design platform, provides a straightforward way to solve this issue—and avoid hours of manual editing or failed topologies. In this guide, we’ll walk through how to properly renumber chains and residues after creating multiple replicas of a protein system using SAMSON’s Martinize2 Extension.
Step 1: Renumber Residue IDs
After creating your copies, right-click the structural model in the SAMSON Document view and choose:
- Structural model > Renumber residues and structural groups
In the dialog that appears, leave the default value to start from residue 1 and click OK.
Step 2: Renumber Chain IDs
Next, still in the context menu of the structural model, choose:
- Structural model > Renumber chain IDs
In the ensuing dialog, default to starting at 0 and click OK.
Step 3: Rename Chains to Ensure Unique Names
Even after renumbering, chain names might still be the same. SAMSON allows you to rename each chain directly:
- Select a chain in the Document view and press F2, or right-click and choose Rename.
You can also rename chains via the Inspector for batch edits:
Why This Matters
Skipping these steps can result in failed topology generation, broken simulations, or incorrect CG models. Ensuring that each chain and residue has a unique identifier helps Martinize2 to cleanly process your models and export valid GROMACS input files without ambiguity.
Once done, you’re ready to proceed with CG model generation as usual via the Martinize2 Extension. Whether you’re working on systems with 2 or 200 protein replicas, these small precautions can save hours and make your workflow much smoother.
Learn more about the modeling process on the official Martinize2 Extension documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.