APBS 1.4.2.0 (2016-01) — APBS-PDB2PQR 1.6 documentation

# APBS 1.4.2.0 (2016-01)

## Binary builds

Binary releases may be found on GitHub and on SourceForge.

## New features

- Poisson-Boltzmann Semi-Analytical Method (PB-SAM) packaged and build with APBS.
- New Geometric flow API and improvements: https://github.com/Electrostatics/apbs-pdb2pqr/issues/235
- Support for BinaryDX file format: https://github.com/Electrostatics/apbs-pdb2pqr/issues/216
- SOR solver added for mg-auot input file option.
- DXMath improvements https://github.com/Electrostatics/apbs-pdb2pqr/issues/168 and https://github.com/Electrostatics/apbs-pdb2pqr/issues/216
- Test suite improvements:
  - APBS build in Travis-CI
  - Geometric Flow test added.
  - Protein RNA test enabled https://github.com/Electrostatics/apbs-pdb2pqr/issues/149
  - Intermediate result testing https://github.com/Electrostatics/apbs-pdb2pqr/issues/64
- Example READMEs converted to markdown and updated with latest results.

## Bug fixes

- OpenMPI (mg-para) functionality restored: https://github.com/Electrostatics/apbs-pdb2pqr/issues/190
- Fized parsing PQR files that contained records other than ATOM and HETATM: https://github.com/Electrostatics/apbs-pdb2pqr/issues/77 and https://github.com/Electrostatics/apbs-pdb2pqr/issues/214
- Geometrix Flow boundary indexing bug fixed.
- Build fixes:
  - Out of source CMake build are again working.
  - Python library may be built: https://github.com/Electrostatics/apbs-pdb2pqr/issues/372
  - CentOS 5 binary builds for glibc compability.
  - Pull requests merged.
- Removed irrelevant warning messages: https://github.com/Electrostatics/apbs-pdb2pqr/issues/378

## Notes

- The following packages are treated as submodules in APBS:
  - Geometric Flow has been moved to its own repository: https://github.com/Electrostatics/geoflow_c/
  - FETk has been cloned: https://github.com/Electrostatics/FETK/
  - PB-SAM lives here: https://github.com/Electrostatics/PB-SAM/
- Added 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 is also an issue for CentOS 5.
- BEM is temporarily disabled due to build issues.
- Geometric Flow build is currently broken on Windows using Visual Studio.