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.