Quickly Generate Multiple Protein Replicas for Coarse-Grained Modeling in SAMSON

Running coarse-grained (CG) simulations of biomolecules often requires building systems with multiple copies of the same protein. Whether you’re simulating crowded cellular environments or studying aggregation processes, creating and managing these replicas correctly can be time-consuming and error-prone.

Fortunately, SAMSON provides an efficient and visual way to generate multiple protein replicas and prepare them for coarse-grained modeling using the Martinize2 Extension. Below, we’ll walk you through how to do this using the Ubiquitin protein as an example.

Step-by-step: Creating Multiple Replicas

1. Make Copies of the Protein Chain

First, select the chain(s) from your loaded structure. Copy and paste using Ctrl/Cmd + C and Ctrl/Cmd + V. New chains will be created directly on top of the original.

Chain copy

2. Move Each Replica

Select each newly created chain and use the global move editor (shortcut K) to position it elsewhere in the scene.

Create replica

You can also copy and move multiple chains simultaneously:

Create multiple replicas

3. Ensure Unique Residue and Chain IDs

Once your replicas are positioned, it’s important to ensure that each one has unique residue and chain identifiers. This prevents issues during topology generation.

  • Renumber residue IDs: Right-click on the structural model > Structural model > Renumber residues and structural groups.
  • Renumber chain IDs: Right-click on the structural model > Structural model > Renumber chain IDs.
  • Rename chains: Use F2 in the document view or the Inspector.

Rename chains

Why This Matters

Manually preparing multiple protein copies in traditional workflows often involves text editing of large coordinate files or using command-line tools with strict input formats. SAMSON makes this visual and interactive, helping you avoid mistakes while speeding up system setup.

Once your replicas are in place and appropriately renumbered and renamed, you can return to the Martinize2 workflow to convert them into coarse-grained models just like you would with a single structure.

To learn more about the coarse-graining workflow in SAMSON using Martinize2, check out the full documentation page: Martinize2 in SAMSON.

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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