NBCR Summer Institute: Molecular Electrostatics

This material prepared by Nathan Baker (group home page, e-mail) and is for educational purposes. Please do not redistribute without permission.

2006 materials have been moved here.

Continuum electrostatics lectures

• Lecture notes (PDF, 4 per page, 18.9 MB)
• Lecture notes (PDF, 1 per page, 18.9 MB)

APBS tutorials

1. Visualizing biomolecular electrostatics
2. Protein titration state calculations

Other resources

• APBS
  • Home page (external website)
  • User guide (HTML)
  • Tutorial (HTML)
  • Standard example/test suite (directory)
  • Older crown ether binding energy calculations -- explicit/implicit solvent comparison. Requires AMBER for full lab. (HTML)
  • Older MM/PBSA drug-protein binding energy calculations. Requires GROMACS for full lab. (HTML)
• PDB2PQR
  • Home page (external website)
  • User guide (HTML)
  • Examples/tutorial (HTML)
• VMD home page (external website)
• PyMOL home page (PyMOL)

Things for the TSRI lab

• Non-MPKG distribution
• MPKG distribution