Calculating non-linear normal modes

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension is an advanced version of the Normal Modes Analysis SAMSON Extension also available on SAMSON Connect.

This SAMSON Extension computes nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134).

First, you have to import a structure. For this tutorial I used the 1VPKPDB entry. Then, you launch the NMA module and indicate the desired number of modes, interactions cutoff distance, and potential function. For now, the elastic network model potential is the one that is available but more potential functions, like the Gaussian network model, will be added in the future.

You can compute normal modes on a group of residues (that may be easily selected using SAMSON’s selection filter) or on the entire structure by selecting the structure in the Data Graph Node.

During computation, a progress bar is displayed and the computation steps are shown in the SAMSON status bar. A few seconds later, the result of the computations is displayed in the Output group box:


Moving a slider will instantaneously display the mode specific motion of the structure:

Note how each mode also has a specific checkbox and reset button. Modes can be combined (when their checkbox is checked) and applied to the structure using the play/pause button. Note that, during motion, the unchecked sliders can still be manually modified. Therefore, the motion obtained from this modification will also be displayed during the trajectory:

While the modes motions are applied to the structure, real time minimization can be activated, using one of three available minimization algorithms:

Mode sliders can be reset to zero either independently using their corresponding reset button or all simultaneously using the reset all button. Also, all checked modes can be unchecked using the clear button, while the update button applies the values of the sliders to the structure:

During motion, the type of transformation applied can be either linear (translations only) or non-linear (translations and rotations). And the scaling factor can be increased or decreased to change the amplitudes of the motion:

The motion speed can be modified while the motion type can be harmonic or not. Forward and backward steps buttons can be used to navigate through the trajectory step by step:

Structure definition

In the Normal Modes Advanced module, you can find the best combination of Normal Modes that can open/close a defined pocket. This definition can contain residues or atoms.

In the “Structure Definition” tab you can define a target structure and find the best combination of modes that will reach this target structure.

Save/export a resulting conformation

When an interesting conformation of the structure is found, you can save it in different ways.

First you can store a conformation of the structure in the document layer (shortcut C). With SAMSON conformations you can quickly restore the saved conformation of the structure:

However, using SAMSON conformations, you will not be able to superpose several states of the structure. For this kind of operation, you need to create a SAMSON structural model. To do that, select the entire structure, or only part of it, then click on the create button of the NMAL app. You can also export the current structure as a PDB file using the export button:

You can store the entire trajectory by going to the save frames tab of the module. Once the saving interval has been set, you can either store the trajectory as a set of conformations by clicking on the store button or export the trajectory as PDB files using the export button. By double-clicking on the conformation node we can directly display it. Also, the SAMSON conformations that represent the trajectory can be removed using the remove button:

It is also possible, by clicking on the Path button, to store the entire trajectory in the new SAMSON trajectory node. We can start and pause the playing of the trajectory by double-clicking on the trajectory node.

Finally, note that the trajectory and the conformations will be saved using the current settings of the calculations tab. These settings include the motions corresponding to the checked modes, the current slider value of the checked modes, the value of the scaling factor, the motion type (harmonic or not) and, of course, the saving interval.
If you have any questions or feedback, please use the SAMSON forum.

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