Streamlining Coarse-Grained Molecular Models with Martinize2 in SAMSON

For molecular modelers, working on large biomolecular systems can be challenging, especially when simulations become resource-intensive and time-consuming. One effective solution to this problem is transitioning atomistic structures into coarse-grained (CG) models, which simplify the representation of molecules and allow for faster computations. If you are looking for a robust and straightforward way to generate these CG models, SAMSON’s Martinize2 extension is here to help. Let’s delve into how you can create CG models and GROMACS topology files efficiently using Martinize2 in SAMSON.

The Advantage of Coarse-Grained Models

CG modeling reduces the complexity of molecular systems by grouping multiple atoms into beads. For example, all backbone atoms of an amino acid can be represented as a single bead. This dramatically simplifies the molecular system, enabling faster simulations, reduced computational costs, and the ability to analyze larger systems.

Getting Started: What You Need

Before you can begin generating CG models, here are the prerequisites:

• Add the Martinize2 extension from the SAMSON Connect Marketplace.
• Start with a clean atomistic structure. If necessary, use Protein Preparation & Validation to prepare your structure before coarse-graining.
• This tutorial uses Ubiquitin protein (PDB code 1UBQ) as an example, but you can use your own structure following the same steps.

Step-by-Step: Building a Coarse-Grained Model

1. Load the Atomistic Structure: Open your atomic system in SAMSON. You can even fetch a PDB structure directly using the Home > Fetch option and entering the PDB code.
2. Prepare the System: Use the Home menu > Prepare option to remove unnecessary components like water, ions, or ligands. A prepared structure optimizes the quality of the CG model. The image below illustrates the preparation process:

   

3. Access Martinize2: Open the Martinize2 app from the Home > Apps menu or by using the search functionality.
4. Select Your System: Choose the structural model you want to coarse-grain from the document view in SAMSON. This step ensures Martinize2 uses the correct input for the modeling. See the example below:

   

5. Configure Martinize2 Options: Set up key parameters such as the force field (martini3001 by default) and position restraints (e.g., on backbone atoms). Hover over the options to access tooltips for additional explanations. You can always reset to default values if needed. Here’s how the Martinize2 options panel looks:

   

6. Define the Output Directory: Select the folder where the resulting CG model and associated files will be stored.
7. Create Coarse-Grained Models: Click the Create coarse-grained models button. The application will generate output files such as .pdb, .gro, and topology files (.top, .itp) in a timestamped project subfolder within your specified directory. Once the process completes, the generated CG model will be automatically loaded into SAMSON for visualization:

   

Conclusion

By using Martinize2 in SAMSON, creating precise and reliable CG models becomes a streamlined process that reduces simulation bottlenecks and enhances your molecular modeling workflow. From initial system preparation to generating complete GROMACS topology files, Martinize2 simplifies coarse-graining and accelerates your projects.

For more detailed guidance, head over to the documentation page: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/.

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