APBS 0.3.0 (2004-02) — APBS-PDB2PQR 1.6 documentation

# 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