APBS 1.0.0 (2008-04) — APBS-PDB2PQR 1.6 documentation

# APBS 1.0.0 (2008-04)

## New features

- Changed license to New BSD style open source license (see http://www.opensource.org/licenses/bsd-license.php) for more information
- Added in a feature limited version of PMG (Aqua) that reduces the memory footprint of an APBS run by 2-fold
- Modified several routines to boost the speed of APBS calculations by approximately 10% when combined with the low memory version of APBS
- Simplified parameter input for ION and SMPBE keywords (key-value pairs)
- Examples and documentation for size-modified PBE code (Vincent Chu et al)
- Added in “fast” compile-time option that uses optimized parameters for multigrid calculations
- mg-dummy calculations can be run with any number (n>3) of grid points
- Updated PMG license to LGPL
- Added per-atom SASA information output from APOLAR calculations
- Added per-atom verbosity to APOLAR calculation outputs
- Ability to read-in MCSF-format finite element meshes (e.g., as produced by Holst group GAMER software)
- Updated installation instructions in user guide
- Updated inputgen.py to write out the electrostatic potential for APBS input file.

## Bug fixes

- Updated tools/python/apbslib* for new NOsh functionality
- Clarified ELEC/DIME and ELEC/PDIME documentation
- Added more transparent warnings/error messages about path lengths which exceed the 80-character limit
- Fixed small typo in user guide in installation instructions
- Fixed memory leaks throughout the APBS code
- Fixed NOsh_parseREAD errors for input files with r line feeds.
- Fixed a variable setting error in the test examples
- Fixed a bug where memory usage is reported incorrectly for large allocations on 64-bit systems
- Added DTRSV to APBS-supplied BLAS to satisfy FEtk SuperLU dependency
- Fixed a small bug in routines.c to print out uncharged molecule id
- Limited calculation of forces when surface maps are read in