APBS 0.3.0 (2004-02)

News

APBS is now supported by the NIH via NIGMS grant GM69702-01.

Changes that affect users

  • New version of the documentation
  • New directory structure in tools/
  • Finished fe-manual mode for ELEC calculations – this is the adaptive finite element solver
  • Added documetnation for fe-manual
  • New apbs/tools/manip/inputgen.py script to automatically generate input APBS files from PQR data
  • Added new asynchronous mode in mg-para parallel calculations to enable running on-demand and/or limited resources
  • Added new script (tools/manip/async.sh) to convert mg-para calculations in mg-async calculations
  • Added following aliases for some of the more obscure parameters in the input files:
  • chgm 0 ==> chgm spl0
  • chgm 1 ==> chgm spl2
  • srfm 0 ==> srfm mol
  • srfm 1 ==> srfm smol
  • srfm 2 ==> srfm spl2
  • bcfl 0 ==> bcfl zero
  • bcfl 1 ==> bcfl sdh
  • bcfl 2 ==> bcfl mdh
  • bcfl 4 ==> bcfl focus
  • calcenergy 0 ==> calcenergy no
  • calcenergy 1 ==> calcenergy total
  • calcenergy 2 ==> calcenergy comps
  • calcforce 0 ==> calcforce no
  • calcforce 1 ==> calcforce total
  • calcforce 2 ==> calcforce comps
  • Example input files have been updated to reflect this change. NOTE: the code is backward-compliant; i.e., old input files WILL still work.
  • Added new READ options “PARM” and “MOL PDB”, see documentation for more information. These options allow users to use unparameterized PDB files together with a parameter database.
  • Updated the documentation
  • Now include support for chain IDs and other optional fields in PQR/PDB files
  • Added support for parsing PDB files
  • Renamed:
  • amber2charmm -> amber2charmm.sh
  • pdb2pqr -> pdb2pqr.awk
  • qcd2pqr -> qcd2pqr.awk
  • Added a new Python-based pdb2pqr (tools/conversion/pdb2pqr) script that allows users to choose parameters from different forcefields.
  • Updated Python wrappers (tools/python) and added the python directory to autoconf/automake.
  • Reformatted examples/README.html for readability.

Bug fixes

  • Fixed bug in PQR parsing that can cause PDB/PQR files to be mis-read when they contain residues with numbers in their names (Thanks to Robert Konecny and Joanna Trylska)
  • Fixed bug when writing out number/charge density: unrealistic densities reported inside iVdW surface.
  • Fixed bug in VMD read_dx utility
  • Invalid map IDs now result in an error message instead of a core dump (thanks to Marco Berrera)
  • Modified mechanism for cubic-spline output, fixing a bug associated with zero-radius atoms
  • Fixed omission of srfm in sections of documentation (thanks to Sameer Varma)
  • Made autoconf/automake configure setup more robust on Solaris 8 platforms (thanks to Ben Carrington)

Changes that affect developers

  • New docuemtnation setup
  • New tools/ directory structure
  • Changed Vgreen interface and improved efficiency
  • Changed Vopot interface to support multiple grids
  • Added several norm and seminorm functions to Vgrid class
  • Altered –with-blas syntax in configure scripts and removed –disable-blas
  • Documented high-level frontend routines
  • Cool new class and header-file dependency graphs courtesy of Doxygen and Graphviz
  • Added substantial mypde.c-based functionality to Vfetk
  • Moved chgm from PBEparm to MGparm
  • Minor changes to Vfetk: removed genIcos and added genCube
  • FEM solution of RPBE working again (see test/reg-fem) and is probably more up-to-date than test/fem
  • Updated API documentation
  • Changed many NOsh, FEMparm, MGparm variables to enums
  • Changes to Valist and Vatom classes
  • Fixed minor bugs in documentation formatting
  • Made Vopot more robust
  • Created Vparam class for parameter file parsing
  • Added vparam* parameter database flat files to tools/conversion/param