How do I visualize the electrostatic potential around my biomolecule?

From APBS software documentation wiki

There are several ways to visualize electrostatic properties and potentials calculated by http://www.poissonboltzmann.org/apbs. This section walks through some of the basic ways to calculate and visualize http://www.poissonboltzmann.org/apbs electrostatics using other programs with graphical user interfaces.

VMD

The VMD molecular graphics software package provides support for both the execution of APBS and the visualization of the resulting electrostatic potentials. Documentation on the APBS interface has been provided by the VMD developers at http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/. We will supplement this with a basic demonstration of how go from a PDB entry to a plot of structure and potential in VMD using APBS.

Note: This tutorial was written using VMD 1.8.5.

Generating the PQR

We'll perform this example with arc repressor (PDB ID 1MYK), a DNA binding protein. The first step in the visualization process is generating a PQR file for use with VMD and APBS. Please follow the directions in the "How do I get my structures ready for electrostatics calculations?" section to generate a PQR file for this structure.

Loading the PQR

Load the PQR file you just created into VMD (File → New molecule... in the VMD Main window). Adjust the molecule to the desired view. Depending on the force field you used in PDB2PQR, you may notice that VMD is displaying some strange bonds. When a PQR file is loaded into VMD, bond distances are inferred from the PQR radii. These radii were chosen for continuum electrostatics calculations, not visualization, and therefore some of the radii are artificially small. Don't worry if some of the bonds appear a bit strange (hide the hydrogens if it really bothers you).

Running the electrostatics calculation

1. Choose Extensions → Analysis → APBS electrostatics in the VMD Main window. A new APBS Tool window should appear.
2. Choose Edit → Settings... in the APBS Tool window and set the path to your local copy of the APBS executable. Hit OK to close this window.
3. Select the "0" calculation from the "Individual PB calculations (ELEC):" window. Hit the Edit button. Adjust the APBS settings here as you desire. The defaults are usually fine, although it may be useful to edit the ions to adjust the ionic strength used in the calculation. Hit OK when you're done.
4. You're now ready to run the calculation. Hit Run APBS in the APBS Tool window. Check the VMD Console window for information about the job while it's running. When the job is finished, a "APBSRun: Load APBS Maps" window should appear. Select "Load files into top molecule" and hit OK.

You're now ready for electrostatics calculations.

Electrostatics visualization

Isocontour visualization

One of the most popular visualization methods is the isocontour.

1. First, choose Graphics → Representations... from the VMD Main window.
2. Hit the Create Rep button and change Drawing Method to "Isosurface".
3. Change Draw from "Points" to "Solid Surface" and Material to "Transparent".
4. Note that the current isovalue is 0; change this to 1 (or 5 or 10 or whatever) depending on your personal preferences.
5. To continue the lonstanding tradition of electrostatic potential coloring, choose "ColorID 0" for the Coloring Method.
6. For the negative isocontour, hit "Create Rep" and select the newly created representation. Change the isocontour value to -1 (or 5 or 10...) and the ColorID to 1.

At this point, you probably have an image that looks something like this (note that I changed the surface to points to make the figure a bit cleaner):

Visualizing surface potentials

Another popular method of electrostatic potential visualization maps the electrostatic potential to the biomolecular surface. Before proceeding, you may want to delete the two isocontours you just created using the Delete Rep in the Graphical Representations window.

1. Go to the Graphical Representations window (Graphics → Representations... from the VMD Main window) and create a new representation of the molecule with the Create Rep button.
2. Go to the "Draw style" tab of the Graphical Representations window and change Drawing Method to "Surf" and Coloring Method to "Volume".
3. Go to the "Trajectory tab" of the Graphical Representations window and change the "Color Scale Data Range:" to -10 to 10 (or whatever your favorite values are).
4. Based on your version of VMD and your personal preferences, you might want to change the color scale for this image. Go to Graphics → Colors... in the VMD Main window and select the "Color Scale" tab from the new "Color Controls" window. The traditional coloring scheme for electrostatics is "RWB" (in the Method menu).

Your molecule now probably looks like this:

For your information, VMD appears to generate a molecular or Connolly type of surface rather than the solvent-accessible or Lee-Richards surface I personally prefer for this type of visualization.... It is usually more useful to plot the surface potential on a more inflated surface than the molecular surface; for example, use an inflated van der Waals surface or the solvent-accessible surface. If you use the molecular (e.g. Connolly) surface, it is not far from just plotting positively- and negatively-charged residues.

Visualizing field lines

Field line visualization can be a very informative way to examine the local intensity of electric fields and related gradient quantities in the context of the biomolecular structure. For this example, we'll use the mouse acetylcholinesterase (mAChE; PDB ID 1MAH) since the field lines around this molecule are often used to interpret preferred mechanisms of binding for the positively-charged substrate.

The APBS distribution comes with a pre-processed PQR file for the mAChE structure available in the examples/misc/ directory of the distribution or here.

Loading the molecule

As in previous examples, we start by loading the mache.pqr file into VMD as a PQR file. Once this is loaded, go to the Graphics → Representations window and change the Drawing Method to NewCartoon or some other view that's a bit less cluttered. At this point, your VMD window might look something like this:

Running the electrostatics calculation

The APBS electrostatics calculation is performed essentially as described in the above examples. However, for field lines, it is generally useful to increase the calculation box dimensions before running APBS. After setting up the APBS calculation as described above, select the "0" calculation from the "Individual PB calculations (ELEC):" window. Press the Edit button and set

• Coarse Grid to: 170 170 170
• Center: 0 mache.pqr
• Fine Grid to: 105 105 105
• Center: -24.29 6.6 1.7

You should vary these settings for different problems or to further explore field lines for the mAChE system.

You're now ready to run the calculation. Press Run APBS in the APBS Tool window. Check the VMD Console window for information about the job while it's running. When the job is finished, a "APBSRun: Load APBS Maps" window should appear. Select "Load files into top molecule" and press OK.

Field line visualization

We're now ready to visualize the electric field lines around mAChE:

1. Choose Graphics → Representations from the VMD Main window and press the Create Rep button.
2. Change Drawing Method to "FieldLines"
3. The default parameters for field lines are reasonable but it might be useful to increase the size of the lines and change the density of these lines for easier visualization through the following settings:
   • Size: 2
   • GradientMag: 8.3
   • Min Length: 1.00
   • Max Length: 200.00
4. We're now going to color the field lines by the electrostatic potential value:
   1. Set the Coloring Method to Volume.
   2. Navigate to the Trajectory tab and set the Color Scale Range from -0.5 to 0.5 (or to different values if you want to change the distribution of color along the field line).
   3. Press the Set button for the changes to take effect.

Your VMD window should now show the mAChE molecule with the electric field lines:

PyMOL

The PyMOL molecular graphics software package provides support for both the execution of APBS and the visualization of the resulting electrostatic potentials. We will provide a basic demonstration of how go from a PDB entry to a plot of structure & potential in PyMOL using APBS.

Note: This tutorial was written using PyMOLX11Hybrid 0.99 on a Mac.

Generating the PQR

We'll perform this example with fasciculin-2 (PDB ID 1FAS), a snake neurotoxin which binds the negatively-charged acetylcholinesterase. Please generate the PQR file using the steps outlined in the "How do I visualize the electrostatic potential around my biomolecule?" section.

Load the PQR file you created into PyMOL (File → Open...) and choose your favorite graphical representation of the molecular structure.

Performing the electrostatics calcuation

Go to the Plugin → APBS Tools... to open the APBS calculation plugin.

1. Under the "Main" tab of the PyMOL APBS Tools window, select Use another PQR and either browse to (via the Choose Externally Generated PQR: button) or input the path to your PQR file. This step is necessary to ensure you use the radii and charges assigned by PDB2PQR.
2. Under the "APBS Location" tab of the PyMOL APBS Tools window, either browse to (via the APBS binary location: : button) or input the path to your local APBS binary. It is not necessary to provide a path to the APBS psize.py binary for most biomolecules.
3. Under the "Temporary File Locations" tab of the PyMOL APBS Tools window, customize the locations of the various temporary files created during the run. This can be useful if you want to save the generated files for later use.
4. Under the "Configuration" tab of the PyMOL APBS Tools window, hit the Set grid to set the grid spacings. The default values are usually sufficient for all but the most highly charged biomolecules.
5. Under the "Configuration" tab of the PyMOL APBS Tools window, customize the remaining parameters; the defaults are usually OK.
6. Under the "Configuration" tab of the PyMOL APBS Tools window, hit the Run APBS button to start the APBS calculation. Depending on the speed of your computer, this could take a few minutes. The Run APBS button will become unselected when the calculation is finished.

Note that 0.150 M concentrations for the +1 and −1 ion species are often useful to ensure that electrostatic properties are not overly exaggerated.

Visualize the electrostatic potential

Before proceeding with the remaining steps, you must load the electrostatic potential data into PyMOL. Under the "Visualization" tab of the PyMOL APBS Tools window, hit the Update button.

Electrostatic isocontours

PyMOL makes this step very easy: adjust the positive and negative "Contour" fields to the desired values (usually ±1, ±5, or ±10 kT/e) and hit the Positive Isosurface and Negative Isosurface and Show buttons.

At this point, you probably have a figure that looks something like:

±1 kT/e electrostatic potential isocontours of FAS2 in PyMOL

If the colors are not as you expect, you can change the colors of the objects iso_neg and iso_pos in the main menu. By convention (for electrostatics in chemistry), red is negative (think oxygen atoms in carboxyl groups) and blue positive (think nitrogen atoms in amines).

Surface potentials

If you haven't already, hide the isocontours by hitting Positive Isosurface and Negative Isosurface and Hide buttons.

The surface potential is also straightforward to visualize. Set the "Low" and "High" values to the desired values (usually ±1, ±5, or ±10 kT/e) at which the surface colors are clamped at red (-) or blue (+). Check the "Solvent accessible surface" and "Color by potential on sol. acc. surf." buttons to plot the potential on the solvent-accessible (probe-inflated or Lee-Richards) surface. Hit the "Molecular Surface" Show button to load the surface potential.

±5 kT/e electrostatic potential of FAS2 in PyMOL plotted on the solvent-accessible surface.

In my opinion, the solvent-accessible surface tends to reveal more global features of the surface potential. Tighter surfaces (e.g., van der Waals and molecular or Connolly surfaces) provides more information about the shape of the biomolecule but otherwise tend to simply map atomic surface charges onto the biomolecular surface. Thankfully, PyMOL provides an excellent solution to the conflicting need to obtain geometric information from the molecular surface together with useful electrostatic potential information from the solvent-accessible surface. To visualize the molecule in this way, simply uncheck the "Solvent accessible surface" box and check the "Color by potential on sol. acc. surf." box on the "Visualization tab". The result is shown below:

±5 kT/e electrostatic potential from the solvent-accessible surface of FAS2 rendered on the molecular surface. Figure made in PyMOL.

Visualization through APBS Tools2 plugin

There is a new (developmental) version of the PyMOL-APBS plugin called APBS Tools 2, developed by Michael Lerner. Following is a list of new features of APBS Tools2 over APBS Tools plugin of PyMOL:

• It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs.
• It allows you to call through to PDB2PQR directly.
• It has two visualization panels to aid in showing multiple potential surfaces at once.

You can download this plugin from http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py

That should give you a file called apbsplugin.py

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

Note that the plugin will be installed as "APBS Tools2" so that you can continue to use your old version.

Then, follow the same visualization steps above to visualize your biomolecule.

(PyMOL APBS Tools2 works with PyMOL 1.2 and/or newer versions.)