Home > PyMOL > Electrostatic potential

Installation of APBS

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

  1. Access PDB2PQR Server
  2. Upload PDB file or enter PDB ID
  3. Click "submit"
  4. ↓scroll down

  5. 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"

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