Avoid Topology Errors in MARTINI by Renumbering Chains and Residues

If you’ve ever built coarse-grained (CG) models using the MARTINI force field and hit a frustrating error during topology generation, you’re not alone. One common cause? Non-unique residue and chain identifiers in systems that include multiple replicas. Fortunately, SAMSON makes it easy to fix this.

When working with protein replicas—whether duplicated manually, via scripts, or using the Molecular Box Builder—each chain and residue must have a unique identifier. If not, tools like Martinize2 might fail to build CG topologies properly. This post walks you through ensuring proper renumbering and naming inside SAMSON so your MARTINI workflows stay error-free.

Why unique IDs matter

Topology generators like Martinize2 read atomistic structures and produce coarse-grained representations. But they can’t interpret ambiguous residue or chain identifiers—especially when multiple chains share the same name or residue count. These overlapping identifiers confuse index generation and lead to failed runs or incorrect results.

How to renumber chains and residues in SAMSON

After creating copies of your protein structure:

  1. Renumber residue IDs:
    Right-click on the structural model in the document. Select:

    Structural model > Renumber residues and structural groups.

    In the dialog, the default starting value is 1. Leave it and press OK.

    Renumber residue IDs
  2. Renumber chain IDs:
    Again, right-click on the structural model and go to:

    Structural model > Renumber chain IDs.

    The default value is 0. Leave it as is and press OK.

    Renumber chain IDs
  3. Rename chains to ensure unique names:
    Find the chains in the document panel. You can select a chain and rename it by pressing F2, or right-click and select Rename.

    Rename chains in the document

    You can also use the Inspector for batch operations:

    Rename chains in Inspector

Good practices and tips

  • Always check identifiers before running Martinize2 on multi-replica systems.
  • Use meaningful chain names if possible—this helps with debugging.
  • Saving your system after renumbering preserves your work and avoids confusion later.

This simple procedure can prevent a class of problems that often go undetected until late in your CG modeling workflow. Better still, it only takes a few clicks in SAMSON and requires no manual editing of PDB files outside the app.

To learn more about working with Martinize2 in SAMSON, visit the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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