PDB2PQR 1.6 (2010-04)¶
New features¶
Added Swanson force field based on Swanson et al paper (http://dx.doi.org/10.1021/ct600216k).
Modified printAtoms() method. Now “TER” is printed at the end of every chain.
Added Google Analytics code to get the statistics on the production server.
Modified APBS calculation page layout to hide parameters by default and display PDB ID
Added “make test-webserver”, which tests a long list of PDBs (246 PDBs) on the production PDB2PQR web server.
Removed
nlev
frominputgen.py
andinputgen_pKa.py
as nlev keyword is now deprecated in APBS.Added PARSE parameters for RNA, data from: Tang C. L., Alexov E, Pyle A. M., Honig B. Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides. Journal of Molecular Biology 366 (5) 1475-1496, 2007.
Bug fixes¶
Fixed a minor bug: when starting
pka.py
from pdb2pka directory using command like “python pka.py [options] inputfile”, we need to make sure scriptpath does not end with “/”.Fixed a bug which caused “coercing to Unicode: need string or buffer, instance found” when submitting PDB2PQR jobs with user-defined force fields on Opal based web server.
Fixed a bug in
main_cgi.py
, now Opal-based PDB2PQR jobs should also be logged inusage.txt
file.Updated
src/utilities.py
with a bug fix provided by Greg Cipriano, which prevents infinite loops in analyzing connected atoms in certain cases.Fixed a bug related to neutraln and/or neutralc selections on the web server.
Fixed a special case with
--ffout
and 1AIK, where the N-terminus is acetylated.Fixed a bug in
psize.py
per Michael Lerner’s suggestion. The old version ofpsize.py
gives wrong cglen and fglen results in special cases (e.g., all y coordinates are negative values).Fixed a bug in
main_cgi.py
, eliminated input/output file name confusions whether a PDB ID or a pdb file is provided on the web server.Fixed a bug which causes run time error on the web server when user-defined force field and names files are provided.
Fixed a bug in
apbs_cgi.py
: pdb file names submitted by users are not always 4 characters long.