We are pleased to announce the release of APBS 1.1.0. This version of the software contains a number of new features including an Opal-based web services client to allow users to run calculations on remote computers and a new documentation site (http://apbs.wustl.edu/) with an improved user guide and tutorials. A complete list of new features and bug fixes is provided below.
As usual, APBS can be downloaded from http://apbs.sourceforge.net/ and help can be obtained from the APBS-users mailing list (subscribe or browse).
Thank you for your continuing support of APBS.
The APBS Development Team
- NEW FEATURES
- Moved APBS user guide and tutorial to MediaWiki
- Added in support for OpenMPI for parallel calculations
- Added in command line support for Opal job submissions (Code by Samir Unni)
- Allowed pathname containing spaces in input file, as long as the whole pathname is in quotes ("")
- Documented 'make test' and related features
- Modified the function bcCalc to march through the data array linearly when setting boundary conditions. This removes duplication of grid points on the edge of the array and corners.
- Clarified documentation on the IDs assigned to input maps, PQRs, parameter files, etc.
- Updated tutorial to warn against spaces in APBS working directory path in VMD; updated user guide to warn against spaces in APBS installation path on Windows
- 'make test' has been reconfigured to run before issuing make install (can be run from top directory)
- Removed tools/visualization/vmd from tools directory in lieu of built-in support in VMD
- Path lengths can now be larger than 80 characters
- Expanded authorship list
- Added in 'make test-opal' as a post install test (run from the examples install directory)
- Added additional concentrations to protein-rna test case to better encompass experimental conditions used by Garcia-Garcia and Draper; this improves agreement with the published data
- BUG FIXES
- Fixed typos in User Guide (ion keyword) and clarified SMPBE keyword usage
- Fixed typo in User Guide (writemat: poission -> poisson)
- Updated psize.py with to fix inconsistent assignment of fine grid numbers in some (very) rare cases
- Fixed bug with boundary condition assignment. This could potentially affect all calculations; however, probably has limited impact: many test cases gave identical results after the bug fix; the largest change in value was < 0.07%.
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis