Low Mode Vibrational Sampling Panel

Calculate and visualize the low vibrational modes of a structure such as a protein.

To open this panel:

  • click the Tasks button and browse to Biologics → Calculate Vibrational Modes.
  • click the Tasks button and browse to Biologics → Visualize Vibrational Modes.
  • Using
  • Features
  • Additional Resources

Using the Low Mode Vibrational Sampling Panel

Finding large-scale motions in proteins can provide information on the flexibility or rigidity of parts of the protein, on domain movements, or give some clues to biochemical processes. Trajectories from molecular dynamics simulations can show the large-scale motions of proteins, but these simulations are not resolved into individual modes, and they require a large amount of computational resources.

The input structure is minimized first, using the PRCG method for a maximum of 10000 iterations to a gradient convergence threshold of 0.05 kJ mol-1Å-1. This ensures that the structure is at its minimum, which is important for generating the vibrational modes. The vibrational modes are generated as a set of structures sampled at regular intervals along a full cycle of the vibrational mode. The rotational and translational modes are discarded.

Before running the calculation, you should ensure that the protein is properly prepared, using the Protein Preparation Workflow Panel (click the Tasks button and browse to Biologics → Protein Preparation Workflow). You should remove waters and solvent molecules so that you are analyzing just the protein (and its ligands, if any).

To set up the calculation:

  1. Select the number of vibrational modes you want to view in the Number of vibrational modes to view text box.

  2. Set the number of frames to generate per vibrational cycle in the Number of frames per mode text box.

  3. Set the maximum amplitude of vibration in the Vibrational amplitude text box.

  4. Click Run.

A job is started that generates the series of structures for each vibration. The limit on the number of atoms that can be processed depends on the memory available on the machine, but with 4GB of memory, it is about 5000. For example, 1ETT, with about 4800 atoms, runs successfully. The job can take several hours to run, depending on the size of the protein.

To visualize the vibrational modes:

  1. Import the results of the job by clicking Browse and selecting the .com file for the job in the file selector that opens.

  2. Specify the mode you want to view in the Vibrational mode to visualize box.

  3. Specify the duration of each frame, in seconds.

  4. Select Loop to loop continuously through the frames, so that the vibration goes through multiple cycles.

  5. Use the play controls to start and stop the animation.

You can rotate the Workspace during the animation to get a better view of the moving parts of the structure.

The low modes are generated by MacroModel. For more information, see Visualizing Vibrational Modes Generated by MacroModel.

Low Mode Vibrational Sampling Panel Features

Calculate tab

 

Number of vibrational modes to visualize box

Specify the number of vibrational modes to calculate and visualize. The trivial modes (translational and rotational) are not considered.

Number of frames per mode box

Specify the number of frames to generate per vibrational mode. Each frame is a snapshot of the structure at a particular point in the vibration between the classical limits. The full cycle of a vibration is divided evenly to define the coordinates used for the snapshots; thus this number should be divisible by 4.

Vibrational amplitude box

Specify the maximum amplitude of the vibration used in the animation. This is the maximum displacement of the fastest-moving atom. For proteins, the fastest moving atom could potentially move a large distance if the motion involves a long loop, for example. The amplitude choice is somewhat arbitrary: you might for example want to exaggerate the motions to make them easier to see.

Run button

Click this button to run the job to generate the low vibrational modes.

Visualize tab

 

File text box and Browse button

Import the results of a vibrational mode calculation for visualization. Click Browse to navigate to and select the .com file for the job. The text box shows the name of the file. The structures are imported into the project as an entry group.

Vibrational mode to visualize box

Select the vibrational mode that you want to visualize.

Seconds per frame box

Specify the time interval for which the structure for each frame is displayed in the Workspace. This setting controls the speed of the animation. The speed at which the structures can be displayed depends on the size of the structure. For structures of 5000 atoms, an interval of 0.1 sec is possible and produces a reasonable animation.

Loop option

Select this option to loop continuously through the frames, so that the vibration goes through multiple cycles.

Play controls

Use these standard play controls to play or step through structures in either direction.

Go to start
Display the first frame.
Previous
Display the previous frame.
Play backward
Display the frames in sequence, moving toward the first.
Stop
Stop play.
Play forward
Display the frames in sequence, moving toward the last.
Next
Display the next frame.
Go to end
Display the last frame.
Remove Structures From Project button

Remove the structures for each frame from the project. As there may be a large number of large structures, it is recommended that you clean up the project when you have finished examining the vibrational modes. You can also remove the entry group in the Project Table panel.

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