Building several copies of a protein into one molecular system can be useful, but copied chains may carry the same residue IDs, chain IDs, or chain names as the original. Those repeated identifiers can cause problems when generating topology files. A short cleanup step before coarse-graining helps make each replica distinguishable and gives Martinize2 a better-prepared input.
This guide focuses on that practical pain point: arranging multiple copies of a protein and checking their identifiers before creating MARTINI coarse-grained models. Ubiquitin (PDB 1UBQ) is the example in the tutorial, but the same workflow applies to your own protein structure.
1. Create the copies
You can create replicas with the Molecular Box Builder, with a Python script, or manually in SAMSON. For the manual approach, first make sure the atoms are visible. Toggle the structural model visibility off and on if needed; this can make it easier to see what you are selecting and where you place each copy.
Select the chain or chains to copy, then use Ctrl+C / Cmd+C followed by Ctrl+V / Cmd+V. The copy is created in the same position, so move the newly copied chain before making another copy. For example, use the global move editor with the K shortcut. Repeat until you have the desired number of replicas. You can also copy and move multiple chains together.
At this stage, the copies may still overlap if you have not moved them apart. The important next step is not just their placement: each replica also needs distinct identifiers.
2. Make residue and chain identifiers unique
Before topology generation, check that residues have unique IDs and chains have unique IDs and names. If you copied a chain, its identifiers may have been copied too. Renumbering and renaming avoids relying on duplicated labels to distinguish separate replicas.
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Renumber residues: right-click the structural model and choose Structural model > Renumber residues and structural groups. In the dialog, keep the default starting value of
1and click OK. -
Renumber chain IDs: right-click the structural model and choose Structural model > Renumber chain IDs. Keep the default starting value of
0and click OK. -
Give chains unique names: rename each chain in the document, using F2 or right-click and choose Rename. You can also rename chains through the Inspector.
A useful preflight check is to confirm that every replica is present, the chains are positioned as intended, and the residue numbering, chain IDs, and chain names are unique. Save the system once this cleanup is complete so you can return to the prepared structure later.
3. Generate the coarse-grained model
With the replicas prepared, continue through the usual Martinize2 workflow. Prepare the atomistic protein system first if needed, then open Martinize2, select the structural model in the document, and click Set. Each structural model is treated as a separate input model, so replicas that you want processed together should be organized within the same structural model.
Review the options, including the MARTINI force field and whether position restraints should be generated for backbone beads, all beads, or none. Choose a results folder and click Create coarse-grained models. The output includes coarse-grained structure files and GROMACS topology files. For a single input structure, the generated coarse-grained model is loaded in SAMSON.
The key habit is simple: copying a structure is not the end of replica preparation. Unique residue and chain identifiers are part of getting the input ready for topology generation. For the complete workflow and option details, see the Martinize2 tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.