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

sargis

Covers Computation and Visualization of Electrostatic Potential.
Page 1 of 4.
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.

 
by Sargis Dallakyan last modified 2008-03-17 11:18
Contributors: Ruth Huey, Michel Sanner
Molecular Graphics Laboratory, TSRI

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