Dear APBS Users --
APBS 1.2.1 has been released. This is a bugfix release specifically aimed at addressing a problem with certain nonlinear Poisson-Boltzmann calculations. In particular, several users noticed that Poisson-Boltzmann calculations which focused into a low dielectric region would occasionally generate very large (~1E25 kJ/mol) energies. This was due to a bug that caused instability in the nonlinear Poisson-Boltzmann solver. This bug has been fixed in this release.
The full list of changes is:
• Added in warning into focusFillBound if there is a large value detected in setting the boundary conditions during a focusing calculation
• Added in a check and abort in Vpmg_qmEnergy if chopped values are detected. This occurs under certain conditions for NPBE calculations where focusing cuts into a low-dielectric regions.
• Fixed a bug in Vpmg_MolIon that causes npbe based calculations to return very large energies. This occurs under certain conditions for NPBE calculations where focusing cuts into a low-dielectric regions.
More information about APBS as well as download links can be obtained from http://www.poissonboltzmann.org/.
We apologize for this bug and thank you for your continued support of APBS.
The APBS Development Team
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