Creating coarse-grained (CG) models is essential for running molecular dynamics simulations efficiently, especially with force fields like MARTINI. But if you’ve ever worked with multiple replicas of a protein structure—say, for studying multimeric interactions or crowded environments—you might have run into an annoying issue: topology generation errors due to non-unique residue and chain IDs.
Fortunately, the Martinize2 Extension in SAMSON provides an effective workflow to handle replicas correctly before generating coarse-grained models. Here’s a practical walkthrough on how to avoid ID conflicts and ensure your simulation starts on the right foot.
Why Unique IDs Matter
When Martinize2 generates topology files for GROMACS, it expects each residue and chain ID to be unique. If you’ve duplicated a protein structure inside your model, there’s a high chance the IDs are reused, making it unclear which chain or residue belongs where. This can break your simulation setup.
How to Fix This in SAMSON
Once you have your replicas arranged in SAMSON (whether using the Molecular Box Builder, Python scripting, or by manual copying), follow these steps:
1. Renumber Residues
Right-click on the structural model and choose:
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Structural model > Renumber residues and structural groups |
Start numbering from 1 (default value). This ensures each residue across all replicas gets a unique ID.
2. Renumber Chain IDs
Similarly, right-click on the structural model and select:
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Structural model > Renumber chain IDs |
This provides unique internal IDs which are necessary for topology generation.
3. Give Chains Unique Names
Although renumbering IDs is usually sufficient, it’s also good practice to give your chains readable, unique names. You can:
- Click a chain and press F2 to rename it directly
- Or use the Inspector panel for more detailed changes
Once you’re done with renumbering and renaming, your CG model will be generated without input errors and will also be easier to analyze later.
Bonus: Save Your Work
It’s worth saving your model after renumbering so you don’t lose changes. Export it under a meaningful filename to recall it later.
Conclusion
Handling multiple replicas in coarse-grained molecular simulations can be tricky if chain and residue IDs overlap. The Martinize2 extension in SAMSON helps solve this problem reliably, ensuring your system is ready for GROMACS topology generation and CG simulations without ID conflicts.
To learn more about replica management and model preparation in Martinize2, check out the full tutorial here: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.