Creating Multiple Protein Replicas for Coarse-Grained Modeling in SAMSON

Working with molecular simulations often requires building systems with multiple copies of the same protein. For example, studying aggregation, self-assembly, or phase separation phenomena means that the ability to efficiently generate replicas becomes essential.

If you’ve ever had to create multiple identical chains manually—copying atoms, adjusting names, resolving clashes—you know how tedious (and error-prone) that process can be.

Fortunately, SAMSON provides a user-friendly workflow to generate and prepare multiple protein replicas for coarse-grained (CG) modeling using the Martinize2 Extension. Let’s walk through it.

Why replicas need attention

When dealing with multiple replicas of a protein, it’s not just about duplication. Each replica must have:

  • Unique residue IDs
  • Unique chain identifiers
  • Correct structural positioning (to avoid overlaps)

Without this, CG topology generation tools like Martinize2 may produce invalid or ambiguous topologies.

Step-by-step: Manual replica creation in SAMSON

Here’s how you can generate replicas manually in SAMSON:

  1. Ensure full atom visibility: Toggle the structural model visibility to make all atoms visible.
    Toggle the structural model visibility
  2. Select chain(s) you want to replicate.
    Select chain(s)
  3. Use Ctrl/Cmd + C and Ctrl/Cmd + V to copy and paste. This creates a duplicate chain at the same location.
    Chain copy
  4. Use the Global Move Editor (K) to move the new chain to a different location.
    Create replica
  5. Repeat the process to create as many replicas as you need. You can also select and move multiple chains at the same time.
    Create multiple replicas

If you need more replicas or prefer a more automated approach, you can also use the Molecular Box Builder or scripting.

Fixing identifiers

After duplicating, make sure to:

  1. Renumber Residues:
    Right-click the structural model → Structural model > Renumber residues and structural groups → Start from 1.
    Renumber residue IDs
  2. Renumber Chains:
    Right-click the structural model → Structural model > Renumber chain IDs → Start from 0.
    Renumber chain IDs
  3. Rename Chains:
    Use F2 in the document or rename via the Inspector to give each chain a unique name.
    Rename chains in the Inspector

This setup is critical before passing the system to Martinize2 for CG conversion, ensuring correct topology generation and file export.

Next steps: Coarse-Graining

Once you’ve prepared your replica system and fixed all the identifiers, move on to the CG conversion using Martinize2. You can follow the usual workflow: select system, configure options, and click Create coarse-grained models.

To learn more and follow the full tutorial, visit the original documentation for Martinize2: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/

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

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