APBS 1.4.2.1 (2016-01) — APBS-PDB2PQR 1.6 documentation

# APBS 1.4.2.1 (2016-01)

## New features

- Poisson-Boltzmann Semi-Anlytical Method (PB-SAM) packaged and built with APBS.
- New Geometric flow API and improvements in speed.
- Support for BinaryDX file format.
- SOR solver added for mg-auto input file option.
- DXMath improvements.
- Test suit improvements: * APBS build in Travis-CI * Geometric Flow tests added. * Protein RNA tests enabled. * Intermediate results testing.
- Example READMEs onverted to markdown and updated with latest results.

## Bug fixes

- OpenMPI (mg-para) functionality restored.
- Fixed parsing PQR files that contained records other than ATOM and HETATM.
- Geometric Flow boundary indexing bug fixed.
- Build fixes: * Out of source CMake build are again working. * Python library may be built. * CentOS 5 binary builds for glibc compatibility. * Pull requests merged.
- Removed irrelevant warning messages.

## Notes

The following packages are treated as submodules in APBS: * Geometric Flow has been moved to its own repository. * FETk has been cloned so that we could effect updates. * PB-SAM lives here: https://github.com/Electrostatics/PB-SAM

Added a chat feature for users.

## Known bugs

- Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that does not support C++11. This also and issue for CentOS 5.
- BEM is temporarily disabled due to build issues.
- Geometric Flow build is currently broken on Windows using Visual Studio.