Hello --

APBS 0.3.2 is over 5 years old and there have been many changes since then.  I would encourage you to review the revision history at http://www.poissonboltzmann.org/apbs/release-history; there are any number of reasons why the potential might be different.



On Dec 11, 2009, at 4:25 PM, johanna wrote:


While switching computers our lab recently noticed major differences between electrostatic potentials calculated by an old version of apbs (version 0.3.2) and a new version (apbs 1.2) . What we see is the appearance of "charged holes" in the new version.

What I mean by "charged holes" is that the inside of small cavities on the protein surface acquired strong surfaces charges somewhere between apbs version 0.3.2 and 1.2.
I have attached a png file of 3IKO chain C to illustrate the issue. All calculations were done at the default settings, via plugin in pymol and the program terminated without error.

(428 KB) 3IKO_chainC.png
via the following link(s):


Expiration: Files will be removed on Dec 21, 2009 at 5:17 pm

We have now a heated discussion about these "charged holes" in the lab and are wondering if anybody else noticed them, 

best regards, 

Johanna napetschnig
Graduate Fellow
The Rockefeller University
Blobel Lab / HHMI

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Nathan Baker (http://bakergroup.wustl.edu/)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis