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From: Nathan B. <ba...@cc...> - 2008-01-06 02:59:47
|
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. More information about these modifications and a complete list of changes can be obtained from the PDB2PQR ChangeLog file provided with the source archive. As always, the files can be downloaded from Thank you for your continuing support of PDB2PQR. Sincerely, The PDB2PQR Development Team -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
|
From: Nathan B. <ba...@cc...> - 2007-04-03 13:21:25
|
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.
Thank you for your continuing support of PDB2PQR.
Sincerely,
The PDB2PQR Development Team
|
|
From: Todd D. <to...@cc...> - 2006-06-23 14:48:19
|
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 |
|
From: Todd D. <to...@cc...> - 2006-05-03 19:16:46
|
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. Thanks! Todd Dolinsky |
|
From: Todd D. <to...@cc...> - 2006-04-12 19:19:40
|
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 mak=
e
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 inpu=
t
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.
Please see the ChangeLog for the full list of changes. As you can see
there is far greater flexibility in this version of PDB2PQR, and as
such users are encouraged to update to this new version.
To download the new release please visit
http://pdb2pqr.sourceforge.net/
Thanks for your interest in PDB2PQR!
Todd Dolinsky
|
|
From: Todd D. <to...@cc...> - 2005-12-16 17:47:03
|
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 http://pdb2pqr.sourceforge.net or check out the updated server at the WUSTL mirror http://agave.wustl.edu/pdb2pqr/server.html Thank you for your continuing interest in PDB2PQR! - Todd Dolinsky |
|
From: Todd D. <to...@cc...> - 2005-10-07 15:45:20
|
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. For now please download the new version at your convenience. http://pdb2pqr.sourceforge.net Thanks for your support of PDB2PQR! Todd Dolinsky |
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