This documentation was prepared for a workshop sponsored by the Collaborative Computational Project for Biomolecular Simulation (CCPB) held at the University of York on 9 January 2009 in conjunction with the Biomolecular Simulation 2009 conference. It was presented by Nathan Baker and Kaihsu Tai.
This workshop is designed to introduce the basic concepts and tools associated with computational electrostatics and solvation modeling in biomolecular contexts. Given the biases of the presenters and time constraints, the workshop focuses primarily on using the APBS and PDB2PQR software packages for Poisson and Poisson-Boltzmann electrostatics calculations.
The schedule for this workshop is:
Thee first session of these practicals are designed to introduce the basic concepts associated with electrostatics and solvation calculations using APBS and PDB2PQR. More advanced topics using these tools are introduced in the second session.
The full PDB2PQR distribution should be avalable from
PDB2PQR was designed to facilitate Poisson-Boltzmann calculations, so we will start by working through the features and capabilities of this software in the context of biomolecular solvation and electrostatics. This material is covered in the PDB2PQR tutorial which we will cover in the first part of this practical.
APBS is a tool for the calculation of biomolecular solvation using a Poisson-Boltzmann electrostatic model and a simple model for nonpolar solvation. More information about this software can be found at the APBS homepage and in the APBS user guide.
This portion of the workshop will introduce biomolecular solvation calculations and APBS in a series of simple steps based on answers to the following questions:
Additional APBS examples can be found in the APBS distribution and elsewhere on this wiki.
Each of these topics will be briefly introduced in the workshop. However, due to time limitations, you will need to choose one specific lab to work on during the practical sessions: