For molecular modelers, an often overlooked but critical step in generating accurate protein motion and transition pathways is the quality of the input data. Correctly preparing protein models ensures reliable pathway computations, mitigates errors, and saves valuable time. If you’re getting started with SAMSON’s Protein Path Finder, here’s a step-by-step guide on preparing your system effectively to make the most of this powerful tool.
Why Protein Preparation Matters
Protein motion studies are sensitive to issues such as missing atoms, solvents interfering with results, or incorrect hydrogenation. Without properly prepared input models, the resulting calculations can become physically unrealistic, leading to unreliable insights. A well-prepped protein is the foundation for finding and refining valid transition pathways.
How to Prepare Your Proteins in SAMSON
1. Remove Unnecessary Components
Protein models often include extraneous elements such as ligands, solvents, and ions. These need to be stripped away before processing to avoid unnecessary computational overhead and distorted results.
- To clean your system in SAMSON, navigate to Home > Prepare and remove alternate locations, ligands, solvent, and ions.
2. Add Hydrogens
Adding hydrogens is essential for stabilizing the structure and maintaining fidelity in energy calculations. SAMSON allows you to quickly add missing hydrogens depending on the pH. For specific pH settings or advanced needs, use the PDBFixer Extension.
3. Fix Missing Residues or Atoms
If your protein model has missing residues or side-chain atoms, gaps in the structure can drastically impact simulations. The PDBFixer extension in SAMSON can repair such issues:
- Add missing residues and heavy atoms.
- Ensure consistency in structures when working with multiple input files.
4. Concatenate Conformations
If the start and goal conformations exist in separate files, they need to be combined into one PDB file as separate models. This ensures compatibility with SAMSON simulations:
|
1 2 3 4 5 6 7 |
MODEL 1 ... ENDMDL MODEL 2 ... ENDMDL END |
Note
If you are following the Protein Path Finder tutorial, the provided tutorial sample file is already prepared and consists of a single SAMSON document.
5. Minimize the System
Before pathfinding, minimize your system for stability and reduce energy artifacts. SAMSON allows you to perform this process directly using Edit > Minimize, which applies the Universal Force Field (UFF).
Learn More
By investing time in preparation, you set the stage for effective pathfinding and motion generation between target conformations. To follow detailed steps on protein preparation and validation, refer to SAMSON’s Protein Preparation & Validation tutorial. For exploring protein paths specifically, explore the full Protein Path Finder documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.