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Molecular Electrostatics

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Note: This is the print view with all the tutorial pages on one page. The paginated version is available here, if you prefer that.

Covers Computation and Visualization of Electrostatic Potential.

Quickstart

Describes minimal steps needed to run APBS and visualize the results.
his_ms.png

PMV uses Adaptive Poisson Boltzmann Solver (APBS) to calculate electrostatic properties for molecules.  APBS binaries are included with MGLTools, so there is no need to download and install APBS separately.  We do need, however, molecular structure as an input. I've included in this tutorial HIS.pdb, that contains 3D coordinates for histidine. You can use any other molecule you are interested.

Note, current version of pdb2pqr included with MGLTools fails to conver pdb with a single residue. I've created HIS.pqr using procedure described here.

Here are steps need to run and visualize the results:

  1. Read HIS.pdb: FileRead Molecule select HIS.pdb and click on Open.
  2. Run APBS: ComputeElectrostaticsCompute Potential using APBS Wait until the calculation is complete and you will see this message: “Thanks for using APBS”.  Click on OK.
  3. Color molecular surface by APBS Potential: ComputeElectrostaticsMap Potential to Surface and click OK. This calculates molecular surface for histidine and displays it colored by the electrostatic potential The Color Map Legend shows correspondence between colors and electrostatic potential.

Potential Isocontours

Explains how to display isocontours of an electrostatic potential.

Undo previous command using either EditUndo or by clicking on Undo icon on the Tools bar.  Displaying isocontours of an electrostatic potential is another useful way for visualizing volumetric data produced by APBS. To do that,  click on ComputeElectrostaticsIsocontour Potential. This opens the following widget that allows to change  isovalues, hide one of the isocontours or animate by running through different isovalues.
iso_panel.png

An example of the electrostatic potential around histidine residue visualized as isocontours at +1.0 kT/e (blue) and -1.0 kT/e (red)

If you see gray opaque isocontour instead of the red transparent, this probably means that your camera is floating (). In order to fix this, click on the DejaVu GUI icon on the Toolbar (), then click on the Light button underneath Properties and uncheck the checkbox next to "Two Side".

APBS Setup widget

How-to change parameters.

Open APBS Setup widget: ComputeElectrostaticsSetup.

There are following four tabs in this widget:
  1. Calculation - used for setting up Calculation type,  Boundary conditions, selecting molecules, specifying the output, etc..
  2. Grid – used for setting up grid dimensions.
  3. Physics - contains protein and solvent dielectric constant, etc.
  4. Web Services - used for running APBS remotely.
The widget opens with Calculation tab selected; where one of the most important option to select is the Calculation type. By default, Calculation type is set to Electrostatic potential, which tells APBS to calculate electrostatic potential for selected molecule. Two other options for Calculation type are Solvation energy and Binding energy.

When Calculate type is set to Solvation energy, APBS calculates total energy of a molecule twice, once in a solvent (Esolvent) and once in a vacuum (Evacuum). The Solvation energy is outputted as Esolvent - Evacuum. User can also choose to calculate binding energy between two molecules by setting Calculation type to Binding energy, in which case s/he should provide Molecule1, Molecule2 and the Complex between these two molecules. APBS then calculates the energy for Molecule1 (E1), Molecule2 (E2) and Complex (E3), and outputs the binding energy as E3 - E2- E1.


 Before finishing, have a look at the parameters in the Physics tab that can be changed as needed.

Add-on

Creating animated images for presentation or Web pages.

As described in Part 2 of this tutorial, we can animate isocontours of an electrostatic potential. Here, I'll describe how to save images from this animation that you can later use for presentation or to embed in a website. Click on the Vision icon located on the Toolbar. Use FileClose to close APBSIsoContour network, if present.  Download attached APBSIsoContour_pmvnet.py and open this with Vision. This is modified version of the nework with added Grab Image and Save Image nodes from Imaging library.  Make directory called foo where we can  store saved images.  Click on ComputeElectrostaticsIsocontour Potential and press Animate button. This should create a bunch of images under foo. Now you can use ImageMagick or any other software to make animation from these images. With ImageMagick installed you can simply type animate foo/*.png and save as gif.

 


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