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.