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