Working with Protein Replicas in Coarse-Grained Models

When simulating molecular systems, researchers often need to model multiple copies—or replicas—of the same protein. This is especially relevant for studying concentration effects, protein aggregation, or large-scale interactions. But generating coarse-grained (CG) models for these replicas can become a tedious process if done manually or improperly.

Fortunately, the Martinize2 Extension in SAMSON streamlines this workflow. Let’s explore a typical scenario and how to properly prepare a system with multiple protein replicas for coarse-grained modeling using the MARTINI force field.

Why replica systems can be challenging

When creating multiple protein copies, users often overlook two common issues:

  • Non-unique residue IDs across chains
  • Duplicate or missing chain names or IDs

These issues can lead to errors during topology generation with Martinize2, resulting in failed simulations or corrupted models.

Creating replicas manually in SAMSON

To model a system with, say, several Ubiquitin proteins (PDB: 1UBQ), you need to replicate the existing structure. Here’s how to create them manually:

  1. Toggle visibility of the structural model to ensure all atoms are shown:
    Visible structural model
  2. Select the chain to replicate:
    Select chain(s)
  3. Use Ctrl/Cmd + C and Ctrl/Cmd + V to copy and paste. The replica appears at the same position.
    Chain copy
  4. Use the move editor (shortcut: K) to displace the new chain:
    Create replica
  5. Repeat as needed. You can even move multiple chains at once:
    Create multiple replicas

Preventing topology generation errors

Once all replicas are in place, you must address residue and chain specificity:

  1. Renumber residue IDs:
    Right-click on the structural model > Structural model > Renumber residues and structural groups:
    Renumber residue IDs
  2. Renumber chain IDs:
    Right-click > Structural model > Renumber chain IDs:
    Renumber chain IDs
  3. Rename chains to make sure each has a unique name, either in the Document or via the Inspector:
    Rename chains in the Inspector

These steps avoid name clashes and typing conflicts during topology file generation.

What’s next?

With replicas correctly set up and uniquely labeled, you’re ready to proceed with Martinize2 as usual: selecting the structure, adjusting options, and generating the CG models.

While it might be tempting to skip these preparation steps, ensuring clean chain and residue setup will save you time and prevent downstream issues.

To learn more, view the full documentation on Creating Coarse-Grained Models with Martinize2.

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

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