Continuum Electrostatics Calculations

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• How to compute and visualize electrostatic potential?

Objectives

• How to use APBS electrostatics plugin?

Computing electrostatic potential

Surfaces, isosurfaces, and other representations can be colored by electrostatic potential. Any other volumetric properties such as density can be also used for coloring. Electrostatic potential calculations in VMD are done with the Adaptive Poisson-Boltzmann Solver (APBS). APBS solves the equations of continuum electrostatics for biomolecular systems. This means that it computes electrostatic potential for a solvated protein This program must be made available to VMD by loading the apbs module.

To compute electrostatic potential we need a pqr file which is basically pdb file with charges and radii. This file can be made using PDB2PQR web server or utility programs from the ambertools module.

Considering that we will be learning AMBER, let’s use ambertools. There are two steps involved in creating pqr files from pdb files.

Create pdb file with point charges and radii

1. Using a force field and a pdb file, create a topology file

   module purge
   module load StdEnv/2020 gcc ambertools
   cd ~/scratch/workshop_vmd/example_03
   tleap -f leaprc.RNA.OL3
   

   rna=loadpdb bcl2-1.pdb
   saveamberparm rna bcl2-1.parm7 bcl2-1.rst7
   quit 
   

2. Use the pdb and the topology file to create the pqr file.

   cpptraj bcl2-1.parm7
   

   trajin bcl2-1.rst7
   trajout  bcl2-1.pqr pdb dumpq
   go
   quit
   

Run APBS calculations

Load apbs and vmd modules

module purge 
module load StdEnv/2020 apbs vmd

Compute electrostatic potential

1. Load bcl2-1.pqr.pqr
2. Create a QuickSurf or Surf representation
3. Extensions -> Analysis -> APBS electrostatics. Under Edit you can change calculation settings such as temperature, ion concentration, and dielectric constants. Then Run APBS
4. When prompted choose Load APBS into top molecule
5. Select coloring method Volume
6. Adjust Color scale data range in the Trajectory tab. Try [-10 10]
7. By default potential map pot.dx is saved in /tmp/apbs.xxxxx. You can change the directory in the top bar Edit->Settings.

References

VMD Introductory tutorial

Key Points