APBS: Adaptive Poisson-Boltzmann Solver -- Software for evaluating the lectrostatic properties of nanoscale biomolecular systems.

First, go to the APBS/PDB2PQR home page

We will use the feature 'Calculate solvation properties'

The Documentation tab will guide through the download/installation/use steps. For displaying the reuslts with Pymol or Vmd, look into the 'Using with other programs' link.

Running electrostatics calculations requires a modified PDB file, called PQR file. PQR files have information of atomic (partial) charges. They can be created by OpenBabel (make sure you ask for adding all hydrogens, i.e., making them explicit) or by the program pdb2pqr.

For the tutorial, take your favorite protein and, using both Pymol and VMD, create

• molecular surface colored by the electrostatic potential using the default dielectric constant of 80 for the solvent
• molecular surface colored by the electrostatic potential but setting the dielectric constant to 20 to see the effect of solvent dielectric
• Isocontour surfaces (with a solvent dielectric of 80)
• Anything else that the results obtained suggest to be worth looking at

Last modified: 10/30/2015

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