Effortlessly Create Replicas for Coarse-Grained Modeling in SAMSON

If you are a molecular modeler aiming to create coarse-grained models for systems with multiple replicas, you’ve probably encountered challenges around preparing and organizing replicas of biomolecules. The errors stemming from improper numbering or overlapping structures can significantly disrupt workflows. Fortunately, in SAMSON, preparing replicas is a smooth and structured process that saves time while setting you up for success. This blog post walks you through how to create replicas for coarse-grained model generation using Martinize2 in SAMSON.

Why Work with Replicas?

When modeling large systems or studying multi-protein interactions, you often need to create replicas of the same molecular structure. Yet, ensuring that these replicas are correctly positioned and uniquely numbered is crucial for subsequent topology generation. This workflow eliminates ambiguities that could otherwise compromise your simulations.

Step-by-Step: Creating Replicas in SAMSON

1. Make Structural Models Fully Visible

To start, ensure that all atoms in your system are visible, which helps when selecting and managing replicas. Toggle the visibility of the structural model by unchecking and re-checking the structural model checkbox. This makes the entire structure clear and ready for manipulation.

Toggle the structural model visibility

The result should be a completely visible atomic structure:

Visible structural model

2. Copy and Paste Chains

Select the chain(s) you want to replicate from the structural model. You can do this by clicking on the desired chain. Once selected, perform a simple copy-paste action:

  • Press Ctrl+C (or Cmd+C on Mac) to copy.
  • Press Ctrl+V (or Cmd+V on Mac) to paste.

This will create a duplicate of the chain in the exact same position.

Chain copy

3. Position the New Replica

With the newly-created chain selected, switch to a move editor (shortcut: K for the global move editor) using the toolbar on the left. Move the replica to the desired location within your system.

Create replica

For precision, enable translational and rotational snapping from the top-left corner of the viewport. For example:

Create multiple replicas

4. Repeat as Needed

Repeat the copy-paste and positioning steps until you have the required number of replicas. Don’t worry—you can copy and move multiple chains at once to save time.

Renumbering for Unique IDs

To avoid issues when generating topology files, residues and chains must have unique IDs and names. Here’s how to ensure uniqueness:

1. Renumber Residue IDs

In the document view, right-click the structural model and choose Structural model > Renumber residues and structural groups. Leave the starting ID as 1 in the pop-up and click OK.

Renumber residue IDs

2. Renumber Chain IDs

Right-click on the structural model again and choose Structural model > Renumber chain IDs. Set the starting chain ID to 0 and confirm.

Renumber chain IDs

3. Give Chains Unique Names

If the chains still have identical names, rename them manually:

  • Right-click and select Rename,
  • Or use the Inspector to modify names in bulk.

Rename chains in the document

Final Steps

Once your replicas are created and uniquely numbered and named, save your system. You are now ready to proceed with the Martinize2 coarse-graining workflow.

Ready to Learn More?

To delve further into creating coarse-grained models with Martinize2, visit the full tutorial here.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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