FAQ

This tutorial is designed as a “how to” document to get users acquainted with computational electrostatics calculations using APBS. In order to perform the provided examples, you will need the latest version of APBS. Other requirements are listed in the individual sections. Note that many of the examples in this tutorial can also be run through Opal web-based services. More information is available in the APBS user guide.

This document is under continual construction and revision to provide up-to-date and timely examples. Many of the topics covered in the incomplete sections are also demonstrated in the examples/ directory provided with the APBS distribution. If you have a question that isn’t answered here, please visit the APBS-users mailing list. After you’ve looked for the answer to your question in the archive, please post it to the mailing list.

Frequently Asked Questions

How do I support APBS and PDB2PQR?

How do I calculate a binding energy?

How do I calculate a pKa?

How do I calculate a solvation energy?

How do I get my structures ready for electrostatics calculations?

How do I model the inhomogeneous environment of a membrane?

How do I run a calculation that’s too big for my computer?

How do I run my calculations on someone else’s computer?

How do I use APBS with my external simulation software?

How do I visualize the electrostatic potential?

What values should I use for my grid spacing?

What are the sources of error in my calculation?

What are the units of electrostatic potential?

What does the message “WARNING! Unusually large potential values detected on the focusing boundary!” mean?

What is FEtk?

What is focusing?

What is MALOC?

What is Opal?

What is PMG?