How to Minimize Specific Parts of Molecules in SAMSON

As a molecular modeler, you may often encounter situations where it becomes essential to optimize the geometry of a specific part of a molecule without altering the rest of the structure. In SAMSON, this can be achieved by freezing parts of a molecule before performing an interactive minimization. This article explains how to use this feature to precisely control molecular optimization.

Why Should You Use Freezing?

When minimizing a molecule, there might be circumstances where only a selected region should relax while the other parts remain fixed. For example, you may want to preserve the orientation of a functional group while optimizing atoms in a reactive site. By freezing atoms, you can isolate and focus the optimization process, increasing control and achieving more precise results.

How to Freeze and Minimize

Here’s the step-by-step process to minimize a specific part of a molecule in SAMSON:

  1. Select the whole molecule (or keep the selection empty): Access the selection tool in SAMSON and select the molecule you are working with. If you want all atoms in the molecule to be considered, you can leave the selection empty.
  2. Freeze the unselected part: Go to Edit > Freeze. This freezes the current selection or—if the selection is empty—the entire molecule. Frozen atoms are indicated by a dark blue overlay in the viewport, providing clear visual feedback.
  3. Select the part to optimize: Now, select the specific atoms or regions of the molecule to minimize using SAMSON’s selection tools.
  4. Unfreeze the selected part: Use Edit > Unfreeze. This unfreezes only the selected atoms, keeping everything else in the molecule fixed during optimization.
  5. Start minimizing: Click Edit > Minimize to begin the interactive minimization process. SAMSON’s Universal Force Field (UFF) will be applied to perform energy minimization.

    The interactive minimization preferences

  6. Stop the minimization: Once the desired geometry is achieved, stop the optimization by clicking Edit > Minimize again.
  7. Unfreeze the system: After optimization, unfreeze all atoms by selecting the molecule or leaving the selection empty, and clicking Edit > Unfreeze.

Things to Keep in Mind

Frozen atoms are ignored during minimization and retain their positions. This feature is especially useful for preserving anchor points or specific regions of your molecule. However, note that selecting a single atom from a molecule will cause SAMSON to minimize the entire connected component to which the atom belongs.

Visualizing Results

The frozen atoms are visually distinguishable in SAMSON due to their dark blue overlay in the viewport. For a practical demonstration of minimization with frozen atoms, you can check out the video below:

Conclusion

Freezing atoms allows you to optimize only specific parts of a molecule and achieve highly controlled results. Whether you are refining a drug binding site or preserving crucial functional groups, this functionality is integral to advancing your molecular modeling tasks. To learn more about interactive minimization in SAMSON, visit the official documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at SAMSON Connect.

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