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.