APBS 0.5.1 (2007-07)

New features

  • Replaced APOLAR->glen and APOLAR->dime keywords with APOLAR->grid

  • Deprecated mergedx. Added mergedx2

    • mergedx2 takes the bounding box that a user wishes to calculate a map for, as well as a resolution of the output map. An output map meeting those specifications is calculated and store.
  • Added pKa tutorial

  • Added warning about strange grid settings (MGparm)

  • Fixed a bug in vpmg.c that occured when a user supplied a dielectric map with the ionic strength set to zero, causing the map to not be used.

  • Removed deprecated (as of 0.5.0) tools/manip/acc in lieu of new APOLAR APBS features

  • Added enumerations for return codes, new PBE solver (SMPBE) and linear/ nonlinear types

  • Added in code for Size-Modified PBE (SMPBE)

Bug fixes and API changes

  • Fixed buffer over-run problem
  • Fixed case inconsistency with inputgen.py and psize.py scripts which caused problems with some versions of Python
  • Fixed bug wherein ‘bcfl sdh’ behaved essentially like ‘bcfl zero’. Now we have the correct behavior: ‘bcfl sdh’ behaves like ‘bcfl mdh’ thanks to the multipole code added by Mike Schnieders. Interestingly, this bug didn’t have a major on the large-molecule test cases/examples provided by APBS but did affect the small molecule solvation energies. Thanks to Bradley Scott Perrin for reporting this bug.
  • Added support for chain IDs in noinput.py
  • Fixed bug in noinput.py where REMARK lines would cause the script to fail.