Avoiding Errors When Creating Multiple Replicas for MARTINI Coarse-Graining

Creating molecular dynamics models with multiple protein replicas is a common task for molecular modelers studying crowding effects, self-assembly, or large biomolecular systems. However, a hidden pitfall often emerges when preparing these models for coarse-graining: inconsistent or conflicting residue and chain identifiers. If you’re using the Martinize2 SAMSON Extension to convert an all-atom system into a coarse-grained structure using the MARTINI force field, neglecting proper renumbering and naming can break your topology generation. 🧬

This blog post walks you through how to avoid common errors when creating multiple replicas for MARTINI CG modeling, using tools available directly in SAMSON.

Why chain and residue renumbering matters

Martinize2 assumes that each chain and residue has a unique ID and name. When you copy and paste chains in a modeling environment like SAMSON, chances are all your replicas still share the same identifiers. This can result in overlapping definitions in the resulting topology — a problem that can be time-consuming to debug and fix post hoc.

How to create replicas safely

You can create replicas of your protein chain manually in SAMSON:

  1. Select the chain in the document view.
  2. Press Ctrl+C / Cmd+C and then Ctrl+V / Cmd+V to duplicate it.
  3. While the new chain is selected, enable one of the move editors (e.g. the global move editor with shortcut K) to position the replica.

Create replica

Ensuring unique identifiers

Once you’ve added all your replicas, follow these crucial steps:

1. Renumber residue IDs

Right-click the structural model, go to Structural model > Renumber residues and structural groups.

Renumber residue IDs

In the popup dialog, leave the default (start from 1) and confirm. This ensures that each residue gets a unique index.

2. Renumber chain IDs

Right-click the structural model again, and go to Structural model > Renumber chain IDs.

Renumber chain IDs

This helps prevent conflicting chain identifiers in the coarse-grained files.

3. Rename chains with unique names

Each chain should have its own name. You can rename them:

  • Directly in the document view by selecting and pressing F2
  • Or using the Inspector

Rename chains

Pro-tip: Save as you go

After building your system and ensuring uniqueness in residue and chain information, save your structure. This will let you return to a clean, error-free stage if needed.

Next steps

Once all replicas are in place and identifiers are clean, return to the standard Martinize2 CG creation steps to generate topologies and structures for each protein copy.

By following these small, but essential steps, you can prevent large issues during topology generation and simulation setup. These practices are especially helpful for those working with multimeric systems or simulating environments with high protein concentrations.

Learn more in the full Martinize2 SAMSON Extension documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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