Creating Multiple Protein Replicas in SAMSON without Losing Your Mind

Preparing systems with multiple protein replicas is a common need in coarse-grained molecular modeling, especially when studying self-assembly or concentration effects. Yet, what seems like a simple task—duplicating a single protein structure several times—can quickly turn into a frustrating experience if chain and residue identifiers overlap or make topology generation fail later on.

In this post, we’ll walk through a clean and replicable workflow for generating multiple protein replicas in SAMSON using the Martinize2 Extension. This method ensures that your system remains unambiguous and ready for coarse-graining with the MARTINI force field.

Why identifiers matter

If you create several copies of a protein, you’ll want to avoid duplicated residue numbers and chain identifiers. Overlapping IDs can cause errors or strange behaviors during coarse-graining and simulation setup in tools like GROMACS. Fortunately, SAMSON provides an easy way to cleanly rename and renumber your structural elements.

Manual replication workflow

Let’s take the example of the Ubiquitin protein (1UBQ) and create a few clean replicas:

  1. Toggle atom visibility to ensure all atoms are displayed. Uncheck and recheck the structural model checkbox:

    Toggle the structural model visibility

  2. Select the chain from the structure:

    Select chain(s)

  3. Duplicate the chain using Ctrl/Cmd + C and then Ctrl/Cmd + V. The duplicate will appear at the same location.

    Chain copy

  4. Move the new chain using a move editor (use shortcut K for the global move editor). Place it where desired:

    Create replica

  5. Repeat steps 2 to 4 until you have as many copies as needed.

    Create multiple replicas

Assigning unique IDs

Now comes the important part: renumbering.

  1. Renumber residues from the structural model context menu: Structural model > Renumber residues and structural groups. Leave the default start at 1.

    Renumber residue IDs

  2. Renumber chains from the same context menu: Structural model > Renumber chain IDs. Click OK.

    Renumber chain IDs

  3. Rename chain labels to avoid confusion. Use F2 or right-click to rename them in the document view:

    Rename chains in the document

At this point, your system is clean, your chains and residues are uniquely identified, and you’re ready to coarse-grain the system using the Martinize2 extension.

Why this matters

Creating CG models of large systems only works reliably when the input structures are consistent and unambiguous. Duplicate identifiers are difficult to debug, and errors in the topology file can propagate into later stages of your simulation workflow.

By following the above approach, you’ll save time and get a replicable, clean structure ready for coarse-graining. If you later want to automate this, check out the Molecular Box Builder or SAMSON’s scripting options.

To explore further CG modeling workflows, visit the Martinize2 documentation page.

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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