Home > PyMOL > Electrostatic potential

By using PyMOL plugin "APBS", I'll show you how to display electrostatic potential from pdb file.

Installation of APBS

From PyMOL 2.0, APBS and PQR are included, so there is no need to install them.
  1. Access the Download page, and download "apbs-1.1.0-Windows.zip"
  2. Extract the zip file at PyMOL folder


PDB file to PQR file

When calculating the potential of multimers, it is necessary to first edit the PDB file to convert it into a monomer. Although the calculations themselves can be performed, the correct charges cannot be accurately computed.
  1. Access PDB2PQR Server
  2. Upload PDB file or enter PDB ID
  3. Click "submit"
    4. ↓scroll down

  4. Download "****.pqr"



APBS tools

  1. Open PDB file in PyMOL

  2. Plugin → APBS tools

  3. Setting
    4. IN "Main" tab...
    Check "Use another PQR"
    Click "Choose Externally Generated" to select PQR file.

    IN "APBS Location" tab
    Click "APBS binary location" and "APBS psize.py location" to "select apbs.exe" and "psize.py"
    APBS binary location apbs-1.1.0\bin\apbs.exe
    APBS psize.py location apbs-1.1.0\share\tools\manip\psize.py


    Click "Set grid"
    ↓
    Click "Run APBS"


  4. Display
    5. When the calculation is finished...
    1.Uncheck "solvent accessible surface"
    2.Adjust the number of Low, Middle, High
    3.Click "Show"