Simulating systems with multiple copies of a protein—such as membrane-bound proteins or protein condensates—is common in molecular modeling. Coarse-graining these systems using MARTINI force fields can significantly accelerate simulations, but there’s a critical step that often causes confusion: handling multiple replicas correctly before launching the coarse-graining process.
One common challenge molecular modelers face is dealing with duplicate residue and chain IDs when preparing multiple protein replicas for use with tools like Martinize2. Without proper ID management, Martinize2 cannot reliably generate topologies and coarse-grained (CG) models, especially when preparing simulations in GROMACS.
What’s the issue?
When you create multiple copies of a protein in a system—say, to simulate how they aggregate or interact—each chain might get duplicated with the same identifiers. This leads to conflicting chain IDs and overlapping residue numbers, which causes Martinize2 to fail or produce incorrect topologies.
The solution: Renumbering and Renaming
Fortunately, SAMSON provides an intuitive set of tools to properly set up your system before sending it into Martinize2. Here’s how to fix the replica ID issue step-by-step.
1. Renumber Residue IDs
Right-click on your structural model in the document view, then navigate to:
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Structural model > Renumber residues and structural groups |
Use the default starting value (1) and apply. This ensures each residue across all chains has a globally unique number.
2. Renumber Chain IDs
Next, right-click again on the structural model and choose:
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Structural model > Renumber chain IDs |
This assigns each chain a unique letter ID, resolving ambiguity in chain references.
3. Rename Chains Clearly
Use F2 or right-click any chain to rename it, helping you keep track of replicas visually and functionally. You may also do this via the Inspector panel.
Why it Matters
Failing to renumber residues or chains might not produce errors right away—but it may lead to incorrect or faulty topologies that compromise your entire simulation workflow. Properly preparing your replicas guarantees that each chain is uniquely handled by Martinize2, avoiding merge issues and simulation errors in later stages.
After this preparation, you’re ready to proceed with Martinize2 the same way you would for a single protein structure. All replicas will be processed into their respective CG models without conflict.
To see the complete workflow in context and learn how to carry out this process in SAMSON, check out the full tutorial page at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.