Managing Protein Replicas for Coarse-Grained Simulations in SAMSON

When working with coarse-grained molecular simulations, a common challenge is preparing systems that include multiple replicas of the same protein. This is often necessary for simulating crowded environments, large systems, or performing statistical analyses across multiple chains. However, creating and organizing these replicas can be frustrating — especially when topology generators require uniquely named and renumbered chains and residues.

If you’re using the Martinize2 Extension in SAMSON for generating MARTINI-compatible coarse-grained models, there’s a streamlined way to handle this.

Why unique chain and residue IDs matter

Many molecular simulation engines (especially GROMACS, frequently used with MARTINI force fields) require input structures to have unique identifiers for residues and chains. If replicas share names and numbering, Martinize2 may either fail to generate topologies or create ambiguous results.

Creating multiple replicas: a step-by-step workflow in SAMSON

If you want to manually prepare multiple replicas of your protein, here’s how you can do it safely and efficiently inside SAMSON:

1. Make all atoms visible

This helps during the copy-paste steps. Toggle the structural model visibility to ensure you’re seeing every atom:

Visible structural model

2. Copy and move chains

Use Ctrl+C / Ctrl+V (or Cmd+C / Cmd+V on macOS) to duplicate a chain. Use SAMSON’s move editors (press K for global move) to reposition the new chain in 3D space.

Create replica

Repeat until you have the desired number of replicas. You can even select and manipulate multiple chains at once:

Create multiple replicas

3. Renumber and rename

Once you’ve duplicated chains, it’s time to ensure residue and chain IDs are unique:

  • Renumber Residue IDs: Right-click the structural model > Structural Model > Renumber residues and structural groups. Leave default value as 1.
  • Renumber Chain IDs: Right-click the structural model > Structural Model > Renumber chain IDs. Leave default value as 0.
  • Rename Chains: To avoid conflicts, give each chain a unique name via F2 or right-click > Rename.

Renumber residue IDs

Rename chains in the Inspector

What’s next?

Once the replicas are correctly structured, just follow the usual steps to create coarse-grained models using Martinize2. Each replica will be processed individually and output with proper topology and structure files.

This helps avoid manual file editing, improves reproducibility, and reduces the risk of errors during simulation setup.

To learn more and follow step-by-step instructions, read the full documentation: Martinize2 Extension guide.

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

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