PDB2PQR / News: Recent posts

PDB2PQR 1.8 released

We are pleased to announce the release of PBD2PQR 1.8. This version includes support for the new PROPKA 3.0 pKa software, several improvements to the command line extensions functionality, as well as improvements to the PDB2PQR web server. A full list of changes is available in the release history page.

As usual, PDB2PQR can be run through the web or downloaded for use on your computer. Access to both the web server and the downloadable software is available at http://www.poissonboltzmann.org/pdb2pqr/d.... read more

Posted by Nathan Baker 2012-01-26

PDB2PQR 1.7.1

Dear PDB2PQR users --

We are pleased to announce the release of PDB2PQR 1.7.1. This release contains several new features and bug fixes which are described in detail at http://goo.gl/w0BxD. Among these changes are several important features which should be of broad interest to the community.

The primary URL for APBS Opal support has changed to leverage services provided by the National Biomedical Computation Resource (http://nbcr.net/). This provides additional computational resources to users who are interested in running calculations on remote resources.
Added more JMol controls for visualization.
Improved error reporting.
Fixed many bugs in both the command line and web version.
Improved behavior of –userff and –usernames command line switches for user created force fields. –usernames now works properly. See http://goo.gl/pXNNZ
The new version of PDB2PQR can be downloaded from http://www.poissonboltzmann.org/pdb2pqr/d... read more

Posted by Nathan Baker 2011-08-07

PDB2PQR 1.7 released

Dear APBS and PDB2PQR users --

I am happy to announce the release of PDB2PQR 1.7 which includes two major updates:

* For PDB2PQR web interface users: the JMol web interface for APBS calculation visualization has been substantially improved, thanks to help from Bob Hanson. Those performing APBS calculations via the PDB2PQR web interface now have a much wider range of options for visualizing the output online -- as well as downloading for offline analysis.... read more

Posted by Nathan Baker 2010-10-13

PDB2PQR 1.6 released

Dear PDB2PQR users --

We are pleased to announce the release of PDB2PQR 1.6. This version has several new features as well minor fixes to reported bugs. A complete list of changes is provided below. For more information about the new release, to download binaries, or access the PDB2PQR web servers, please visit http://www.poissonboltzmann.org/pdb2pqr

Thank you for your continuing support of the PDB2PQR software.... read more

Posted by Nathan Baker 2010-04-07

PDB2PQR 1.4.0 released

Dear PDB2PQR users --

We are pleased to announce the release of PDB2PQR version 1.4.0, which contains a number of new features including integration of PDB2PQR and APBS Opal services through remote clusters at NBCR. A complete list of new features and bug fixes is provided below.

As usual, PDB2PQR can be downloaded from http://pdb2pqr.sourceforge.net/ and help can be obtained from the PDB2PQR-users mailing list (subscribe: https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users or browse: https://sourceforge.net/mailarchive/forum.php?forum_name=pdb2pqr-users\).... read more

Posted by Nathan Baker 2009-04-03

PDB2PQR 1.3 released

Dear PDB2PQR users --

We are pleased to announce the release of PDB2PQR version 1.3.0 which contains a number of bug fixes and new features. Major changes include:

* The addition of test suites to verify Python is performing correctly (e.g., "make test" and "make adv-test")
* Easier and more robust configuration and installation
* Integration with Opal for launching and querying remote jobs
* A license change from the GNU Public License to the new BSD license (see http://www.opensource.org/licenses/bsd-license.php for more information)
* Support for input PDB files in additional file formats generated on Windows and older MacOS systems.... read more

Posted by Nathan Baker 2008-01-06

PDB2PQR 1.2.1

Dear PDB2PQR users --

We are pleased to announce the release of PDB2PQR version 1.2.1 which contains a number of bug fixes and new features, including:

* Updated documentation to include instructions for pdb2pka support, references, more pydoc documents.
* Added new support for passing in a single ligand residue in MOL2 format via the --ligand command. Also available from the web server (with link to PRODRG for unsupported ligands).
* Added ligand examples to examples/ directory
* Added native support for the TYL06 forcefield. For more information on this forcefield please see
Tan C, Yang L, Luo R. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. Journal of Physical Chemistry B. 110 (37), 18680-7, 2006.1
* Added a new HTML output page which relays the different atom types between the AMBER and CHARMM forcefields for a generated PQR file (thanks to the anonymous reviewers of the latest PDB2PQR paper).
* Numerous additions to examples directory (see examples/index.html) and update to User Guide.... read more

Posted by Nathan Baker 2007-04-03

PDB2PQR Public Release 1.1.2

Hello Everyone -

I'm happy to announce the public release of PDB2PQR Version 1.1.2.
This is a bugfix release, fixing a couple of bugs that some users have
encountered over the last month.

Current users of version 1.1.1 are recommended to upgrade to the new
version at their convenience.

Thanks for your interest in PDB2PQR!

Todd Dolinsky

Posted by Todd Dolinsky 2006-06-23

PDB2PQR Public Release 1.1.1

Hello Everyone -

I'm happy to announce the release of PDB2PQR version 1.1.1. This is
purely a bugfix release, particularly regarding two known bugs:

* PDB2PQR is now able to recognize atoms from nucleic acids with "*"
in their names
* A bug that caused an unexpected SyntaxError crash during hydrogen
optimization was fixed.

Current users of version 1.1.0 are welcome to update, but only need to
do so if they have experienced one of the above issues.... read more

Posted by Todd Dolinsky 2006-05-03

PDB2PQR Public Release 1.1.0

Hello Everyone -

I am very pleased to announce the public release of PDB2PQR Version
1.1.0. This release includes a number of improvements, most notably:

* Structural data files have been moved to XML format. This should make
it easier for users and developers to contribute to the project.
* Added an extensions directory for small scripts. Scripts in this
directory will be automatically loaded into PDB2PQR has command line
options for post-processing, and can be easily customized.
* Added a --clean command line option which does no additions,
optimizations, or forcefield assignment, but simply aligns the PDB
columns on output. Useful for using post-processing scripts like
those in the extensions directory without modifying the original input
file.
* A --ffout flag has been added to allow users to output a PQR file in
the naming scheme of the desired forcefield.
* Increased the number of options available to users via the PDB2PQR
web server.... read more

Posted by Todd Dolinsky 2006-04-12

PDB2PQR Public Release 1.0.2

Hello Everyone -

I am pleased to announce the release of PDB2PQR Version 1.0.2. This release incorporates a couple of bug fixes and a few new features:

* Users may now supplement existing forcefield parameters with user-defined parameters
* Full support for input files intended for APBS 0.4.0
* An examples directory with a mini-tutorial showing how to use the various features in PDB2PQR.

To download please visit the main PDB2PQR web site at... read more

Posted by Todd Dolinsky 2005-12-16

PDB2PQR Public Release 1.0.1

Hello Everyone -

I am pleased to announce the public release of PDB2PQR 1.0.1.

This is primarily a bugfix release - there was an occasional bug during the hydrogen optimization routines which resulted in waters missing hydrogen atoms. This has now been resolved.

We are actively working toward additional improvements, including a more modular input file interface, additional pKa support, and increased support for ligands. We hope to release these updates in the coming months.... read more

Posted by Todd Dolinsky 2005-10-07

PDB2PQR Public Release 1.0.0

Hello Everyone -

I am pleased to announce the public release of PDB2PQR 1.0.0.

PDB2PQR had been previously available only via a web server or associated with APBS (in the tools/conversion directory), but now is also available for stand-alone download. We have split the development of this project with that of APBS - all future updates to PDB2PQR will be made and released from the PDB2PQR SourceForge page.... read more

Posted by Todd Dolinsky 2005-08-23

PDB2PQR moved to SourceForge

We're happy to announce that we've moved PDB2PQR project development over to SourceForge! This move should facilitate additional development, bug tracking, mailing lists, and more. Feel free to browse the PDB2PQR project site to see what's available.

Posted by Todd Dolinsky 2005-07-26