Efficiently Building Replicas for Coarse-Grained Simulations

When working on molecular simulations, especially when utilizing coarse-grained modeling, a common challenge arises when setting up systems with multiple replicas, like modeling systems with repeated protein units. Creating these replicas manually while ensuring proper numbering and uniqueness is a frequent pain point for molecular modelers.

In this blog post, we will outline how to efficiently create replicas for coarse-grained molecular modeling with the SAMSON integrative platform. This approach helps streamline your workflow, avoids common numbering conflicts, and gets your systems ready for topology generation and simulations.

Step 1: Making Chains Visible

To create replicas, start by ensuring all atoms are visible in the original structural model. This step simplifies selection and manipulation. Toggle visibility by unchecking and rechecking the checkbox of your structural model in SAMSON, ensuring every atom in the structure is displayed:

Toggle the structural model visibility

Once enabled, you should see a fully visible model of your structure:

Visible structural model

Step 2: Creating Replicas

Next, proceed to make copies of your protein chains:

  1. Select the chain(s) you want to replicate from the structural model:

    2. Select chain(s)

  2. Copy and paste the selected chain(s) by pressing Ctrl/Cmd + C and then Ctrl/Cmd + V. This will create a duplicate chain directly within the same structural model, initially placed at the same position:

    3. Chain copy

  3. Use SAMSON’s move tools to adjust the position of the new replica. Activate the global move editor (shortcut: K) to reposition the chain:

    4. Create replica

    Tip:

    You can enable snapping for translational and rotational movements in the top-left corner of the viewport. This feature is handy when arranging multiple chains systematically.

Repeat these steps until you have created the required number of replicas. You can select and move multiple chains simultaneously to save time:

Create multiple replicas

Step 3: Ensuring Unique Residue and Chain IDs

While creating replicas, duplicate chains inherit the exact same chain IDs and residue numbers, which can lead to conflicts in topology generation. Fixing this is a critical step:

  1. Renumber residue IDs by right-clicking the structural model and selecting Structural model > Renumber residues and structural groups:

    2. Renumber residue IDs

    In the pop-up, leave the default starting value as 1 and click OK.

  2. Renumber chain IDs by choosing Structural model > Renumber chain IDs from the context menu:

    3. Renumber chain IDs

    Set the starting value as 0, then press OK.

  3. Finally, rename chains to ensure unique chain names. You can do this directly via the document interface (F2) or using the Inspector:

    4. Rename chains in the document

Saving the system at this point ensures you don’t lose any of your adjustments.

What’s Next?

Once your replicas have been created and properly renumbered, you can proceed to generate coarse-grained models with tools like Martinize2. Detailed steps for this process are outlined in the full documentation.

To learn more about SAMSON’s capabilities, check out the full documentation here: Martinize2 tutorial.

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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