Computation/ calculation and Visualization of Electrostatic Potential

Can be performed by multiple ways:

CHIMERA
PYMOL
PMV (Python Molecular Viewer from MGLTools)

PMV (Python Molecular Viewer from MGLTools)

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 1GU8.pdb, that contains 3D coordinates for "SENSORY RHODOPSIN II". You can use any other molecule you are interested.

Here are steps need to run and visualize the results:

Read 1GU8.pdb: File → Read Molecule select 1GU8.pdb and click on Open.
Run APBS: Compute → Electrostatics → Compute Potential using APBS Wait until the calculation is complete and you will see this message: “Thanks for using APBS”. Click on OK.
Color molecular surface by APBS Potential: Compute → Electrostatics → Map 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.

Comments

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