Creating multiple replicas of molecular structures can be an essential step in preparing for simulations, especially when dealing with systems containing repeated units or multiple copies of the same protein. In SAMSON, this process can be streamlined and enhanced using the platform’s intuitive tools. This article will guide you through the process of manually creating replicas, renumbering chains and residue IDs, and ensuring a seamless workflow.
Why is replica creation important?
For molecular modelers, having precise replicas of molecular structures is essential when assembling systems for simulations. Whether you’re studying multimeric proteins, working with symmetric systems, or setting up coarse-grained models, ensuring that replicas are accurately positioned and uniquely identified avoids issues in file preparation and topology generation for simulation software like GROMACS.
Step-by-step guide to creating replicas manually
Follow these steps to efficiently create and configure replicas using SAMSON:
1. Preparing the structural model
Before creating copies, ensure all atoms in your structural model are visible. To do this, toggle the structural model’s visibility by checking and unchecking the checkbox in the document view, as shown below:
This will display the fully visible atomic structure:
2. Copying chains
Start by selecting the chain(s) you want to replicate within the structural model:
Then, use the keyboard shortcut Ctrl/Cmd + C to copy the chain, and Ctrl/Cmd + V to paste it. A duplicate of the chain will appear in the same position:
3. Positioning the replica
While the new chain is selected, switch to a move editor like the Global Move Editor (shortcut: K) to reposition it. The interface allows for translational and rotational snapping for precise placement:
Repeat this process until you’ve created the desired number of replicas. For efficiency, you can copy and move multiple chains at once:
Configuring replicas for simulation
Once you’ve created the desired replicas, ensure their chains and residues are uniquely identified. This avoids complications when generating GROMACS topologies or other processing steps:
1. Renumbering residue IDs
Right-click on the structural model and choose Structural model > Renumber residues and structural groups. In the dialog that appears, set the starting ID (e.g., 1) and click OK:
2. Renumbering chain IDs
Similarly, right-click and select Structural model > Renumber chain IDs. Use a different starting number (e.g., 0) for the chain IDs:
3. Renaming chains
Ensure chains have unique names either by right-clicking and selecting Rename or by using the Inspector:
Final tips
It’s a good idea to save your system into a file to preserve your work. Once all replicas are uniquely configured, you can proceed with additional steps, such as coarse-graining using the Martinize2 extension.
Accurately configuring replicas ensures a smooth workflow and eliminates errors during topology generation and simulation preparation. For further details, visit the Martinize2 tutorial documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.