Running APBS through the PDB2PQR web portal

Running APBS through the PDB2PQR web portal

Introduction

The PDB2PQR web portal provides support for the execution of PDB2PQR and APBS as well as the visualization of the resulting electrostatic potentials. We will provide a basic demonstration of how to go from a PDB entry to a plot of structure & potential through the PDB2PQR web portal.

Generating the PQR

We’ll perform this example with Fusarium solani cutinase (PDB ID 1CUS), a lipolytic enzyme with a catalytic serine accessible to solvent. Go to the PDB2PQR web portal and enter a PDB ID or upload a PDB file. Choose your options for PDB2PQR and click “Submit”.

On the PDB2PQR result page, click bottom link to run APBS with your results.

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Performing the electrostatics calculation

On the APBS web solver page, click “Launch” to use default parameters for the APBS calculation. If you prefer to run APBS with custom parameters, check the check box and make your own selections.

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Wait until the calculation is complete. Click the bottom link to visualize your results.

Visualizing the electrostatic potential

Please be patient and wait until the visualization applet is fully loaded.

±5 kT/e electrostatic potential of 1CUS rendered on the molecular surface. Figure made through Jmol.

Offline rendering with POV-Ray

Jmol also has the ability to generate scenes for higher-quality offline rendering with POV-Ray. This is particularly useful for transforming the images you generate with Jmol via the PDB2PQR web server into high-resolution figures for publication. These instructions assume that you have POV-Ray installed.

Set up the scene in Jmol to look the way you would like the rendered image to appear.

Right click on the Jmol window and select File -> Export POV-Ray Image.

Save the resulting *.pov and *.pov.ini file in the same directory.

Run POV-Ray and load up the *.pov.ini file. You may wish to edit some of the options in the file (particularly “Width” and “Height” to change resolution) to customize the rendering.

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