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.
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.
Load the PQR file you just created into VMD (
You're now ready for electrostatics visualization.
One popular visualization method is the isocontour.
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):
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.
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.
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
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:
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
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.
We're now ready to visualize the electric field lines around mAChE:
Your VMD window should now show the mAChE molecule with the electric field lines: