Building a system with several copies of the same protein can look straightforward: duplicate the chain, move each copy, and run coarse graining. But if those copies retain the same residue numbering or chain names, topology generation can run into problems. A little bookkeeping before you start can help keep replicas distinct and make the Martinize2 workflow easier to manage.
This walkthrough focuses on preparing multiple protein replicas in SAMSON so Martinize2 can treat them as parts of one input structure. The example uses ubiquitin (PDB 1UBQ), but the same preparation steps apply to other proteins.
First, make the replicas
You can create copies with the Molecular Box Builder, a Python script, or manually. To make a copy by hand, select the chain or chains you want to duplicate, press Ctrl+C (or Cmd+C on macOS), then Ctrl+V (or Cmd+V). The pasted chain appears in the same position as the original, so select the new chain and use a move editor to reposition it.
Repeat the copy-and-move process until you have the desired number of replicas. You can also copy and move several chains together. If it is difficult to select or position the atoms, check that the structural model is visible; the tutorial shows how to toggle visibility before making copies.
Why numbering and names matter
Copies of a protein often begin with identical residue IDs and chain names. That is fine for a single copy, but multiple replicas need distinct identifiers. The Martinize2 tutorial warns that non-unique residue IDs, chain IDs, or chain names can cause issues when creating topologies. In other words, placing the copies in different locations is not enough: they also need to be distinguishable in the structure’s identifiers.
Assign unique identifiers before conversion
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Renumber residues. Right-click the structural model and choose Structural model > Renumber residues and structural groups. In the dialog, leave the default starting value of 1 and click OK.
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Renumber chain IDs. Right-click the structural model again and choose Structural model > Renumber chain IDs. Leave the default starting value of 0 and click OK.
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Give the chains unique names. Rename chains directly in the document with F2 or the context menu’s Rename command, or rename them in the Inspector.
Save the prepared system so you can return to it later. This simple check—unique residue IDs, chain IDs, and chain names—helps prevent avoidable ambiguity when generating topology files.
Then generate the coarse-grained model
Open Martinize2, select the structural model in the document, and click Set. Each top-level structural model is treated as a separate input by Martinize2, so replicas that should be processed together need to be present in the same structural model. Review the available settings, choose a results folder, and click Create coarse-grained models. The extension generates coarse-grained structures and GROMACS topology files, including .top and .itp files. For a single input structure, the generated coarse-grained model is loaded into SAMSON.
After conversion, the results folder also gives you a practical place to inspect the generated files and the log, including the Martinize2 command information. For the complete workflow and option descriptions, see the Martinize2 documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.