APBS 1.2.0 (2009-10) — APBS-PDB2PQR 1.6 documentation

# APBS 1.2.0 (2009-10)

## New features

- Updated NBCR opal service urls from http://ws.nbcr.net/opal/… to http://ws.nbcr.net/opal2/…
- Increased the number of allowed write statements from 10 to 20
- Updated inputgen.py with –potdx and –istrng options added, original modification code provided by Miguel Ortiz-Lombardía
- Added more information on PQR file parsing failures
- Added in support for OpenMP calculations for multiprocessor machines.
- Changed default Opal service from http://ws.nbcr.net/opal2/services/APBS_1.1.0 to http://sccne.wustl.edu:8082/opal2/services/apbs-1.2

## Modifications

- Applied Robert Konecny’s patch to bin/routines.h (no need to include apbscfg.h in routines.h)

## Bug fixes

- Added a remove_Valist function in Python wrapper files, to fix a memory leak problem in pdb2pka
- Fixed a bug in smooth.c: bandwidth iband, jband and kband (in grid units) should be positive integers
- Fixed a bug in psize.py: for a pqr file with no ATOM entries but only HETATM entries in it, inputgen.py should still create an APBS input file with reasonable grid lengths
- Fixed a bug in Vgrid_integrate: weight w should return to 1.0 after every i, j or k loop is finished
- Fixed a bug in routines.c, now runGB.py and main.py in tools/python/ should be working again instead of producing segfault
- Fixed a few bugs in ApbsClient.py.in related to custom-defined APBS Opal service urls, now it should be OK to use custom-defined APBS Opal service urls for PDB2PQR web server installations