This documentation was prepared for lectures and a workshop held August 2009 and sponsored by the National Biomedical Computation Resource. It is based on materials prepared by many others in conjunction with the APBS and PDB2PQR software packages.
Due to a death in the family, Nathan Baker will be unable to attend the NBCR workshop -- I am very sorry to miss this event. I have prepared the materials in these tutorials and will leave the execution in Robert Konecny's very capable hands. I have also provided a voice-over version of the talk I normally give; this is available below. However, if you would like to discuss any of the workshop material or electrostatics/solvation methodology in more detail, please feel free to contact me:
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 presenter and time constraints, the workshop focuses primarily on using the APBS and PDB2PQR software packages for Poisson and Poisson-Boltzmann electrostatics calculation with the following content:
The 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.
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 in the APBS user guide and in the rest of this website.
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: