Working with multiple replicas of a protein system is common practice when setting up coarse-grained (CG) molecular dynamics simulations, especially in studies that require ensemble sampling or crowding conditions. However, a frequent and frustrating pain point for molecular modelers arises when tools like Martinize2 fail to generate correct topologies due to non-unique residue and chain identifiers among the replicas.
Fortunately, SAMSON provides a simple and visual workflow to address this issue. Here’s a step-by-step overview that can help you clone proteins and ensure your system is simulation-ready—without the errors that often occur when replicas aren’t properly renumbered or renamed.
Step 1: Create Your Replicas
You can generate copies of your protein using several methods in SAMSON, including the Molecular Box Builder, Python scripting, or manually:
- Select the chain(s) you want to replicate.
- Press Ctrl/Cmd + C and then Ctrl/Cmd + V to duplicate.
- Use the move editor (e.g., shortcut K) to reposition the new replicas.
Here’s how that looks in action:
Step 2: Renumber Residue and Chain Identifiers
Martinize2 assumes that each atom belongs to a uniquely identified part of the protein. If residues or chains share identifiers across replicas, the topology generator may break or generate incorrect files. To avoid this, follow these steps:
Renumber Residue IDs
Right-click your structural model → Structural model > Renumber residues and structural groups:
Leave the default start value and press OK.
Renumber Chain IDs
Then, go to Structural model > Renumber chain IDs from the same context menu:
Again, use the default values and confirm.
Rename Chains
Optionally, ensure chain names are unique to improve clarity. You can rename chains either in the document view (select and press F2), or through the Inspector tab:
Step 3: Save and Proceed to Martinize2
Once residues and chains are uniquely named and numbered, you can safely proceed to generate CG models using Martinize2. This ensures that each replica is treated independently, and topology generation runs smoothly.
Why This Matters
This renumbering step is easy to overlook, but skipping it can derail an entire modeling session. Instead of digging through broken topology files or cryptic errors, following this workflow helps you maintain a clean and correct simulation setup.
You can learn more from the original documentation for further guidance.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.