PDB2PQR 1.5 (2009-10) — APBS-PDB2PQR 1.6 documentation

# PDB2PQR 1.5 (2009-10)

## New features

- APBS calculations can be executed through the PDB2PQR web interface in the production version of the server
- APBS-calculated potentials can be visualized via the PDB2PQR web interface thanks to Jmol
- Disabled Typemap output by default, added –typemap flag to create typemap output if needed.
- Enabled “Create APBS Input File” by default on the web server, so that APBS calculation and visualization are more obvious to the users.
- Added warnings to stderr and the REMARK field in the output PQR file regarding multiple occupancy entries in PDB file.
- Added more informative messages in REMARK field, explaining why PDB2PQR was unable to assign charges to certain atoms.
- Updated structures.py, now PDB2PQR keeps the insertion codes from PDB files.
- Added “make test-long”, which runs PDB2PQR on a long list (246) of PDBs by default, it is also possible to let it run on specified number of PDBs, e.g., export TESTNUM=50; make test-long
- Updated NBCR opal service urls from http://ws.nbcr.net/opal/… to http://ws.nbcr.net/opal2/…
- Compressed APBS OpenDX output files in zip format, so that users can download zip files from the web server.
- Removed “EXPERIMENTAL” from APBS web solver interface and Jmol visualization interface.
- Updated all APBS related urls from http://apbs.sourceforge.net/… to http:/apbs.wustl.edu/…
- Merged PDB2PKA code, PDB2PKA is functional now.
- Added two new options: –neutraln and –neutralc, so that users can manually make the N-termini or C-termini of their proteins neutral.
- Added a local-test, which addresses the issue of Debian-like Linux distros not allowing fetching PDBs from the web.
- Added deprotonated Arginine form for post-PROPKA routines. This only works for PARSE forcefield as other forcefields lack deprotonated ARG parameters.
- Updated inputgen.py with –potdx and –istrng options added, original modification code provided by Miguel Ortiz-Lombardía.
- Changed default Opal service from http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0 to http://sccne.wustl.edu:8082/opal2/services/pdb2pqr-1.5

## Bug fixes

- Verbosity outputs should be stdouts, not stderrs in web server interface. Corrected this in src/routines.py.
- 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.
- Added special handling for special mol2 formats (unwanted white spaces or blank lines in ATOM or BOND records).
- Added template file to doc directory, which fixed a broken link in programmer guide.