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.

Thank you for your continuing support of PDB2PQR.

Sincerely,

The PDB2PQR Development Team

We have released a new version of the APBS Windows Installer with the following features:

• Ability to customize install path with correct behavior
• Interactive command line interface when double-clicking APBS program

The new installer can be obtained through our downloads page.  Please let us know if you have any questions or concerns about this new installer.

Thank you for your support of APBS.

Dear APBS users --

My apologies for the repeated posts on this subject but I wanted to update you on our troubled transition of the mailing lists to Google Groups.

Unfortunately, it appears that many users have restricted access to Google Groups because of firewalls set by their countries and/or organizations.  Therefore, we will continue to host and archive the lists at two sites: 

• APBS-USERS can be accessed at https://lists.sourceforge.net/lists/listinfo/apbs-users or https://groups.google.com/forum/#!forum/apbs-users
• APBS-ANNOUNCEMENTS can be accessed at https://lists.sourceforge.net/lists/listinfo/apbs-announce or https://groups.google.com/forum/#!forum/apbs-announcements

Messages posted to one list will be cross-posted to the other list.  Archives will also be available for both lists; however, the Google Groups site offers easier searching and browsing mechanisms. 

Thank you for your patience.

Sincerely,

Nathan Baker

In response to several requests we've received for more user-friendly mailing lists that are easier to post, browse, and search, we have moved the APBS mailing lists to Google Groups.

The low-traffic APBS-ANNOUNCE mailing list has moved to https://groups.google.com/forum/#!forum/apbs-announcements and the moderate traffic APBS-USERS mailing list has moved to https://groups.google.com/forum/#!forum/apbs-users.  We will be moving users to the new mailing lists during the month of September 2011.

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

Thank you for your continuing support of PDB2PQR.

Sincerely,

The PDB2PQR Development Team

Dear APBS users --

We are pleased to announce the release of APBS 1.3.  This release contains several new features and bug fixes which are described in detail at http://goo.gl/l0Pt.  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, as described at http://goo.gl/CHZy.
• APBS now supports the ability to write out atom-specific potentials using the "write atompot" keyword in the APBS input file.  This has been an often-requested feature and is described in more detail at http://goo.gl/iEAO.
• APBS now supports the ability to read and write compressed (GZIPped) potential file output using the "write pot gz ..." command (see http://goo.gl/iEAO).
• APBS now provides additional control over the numerical accuracy of the underlying calculations, giving users the opportunity to increase/decrease accuracy to change the speed of their calculations.

The new version of APBS can be downloaded from http://www.poissonboltzmann.org/apbs/downloads.

Thank you for your continuing support of APBS.

Sincerely,

The APBS Development Team

Dear APBS Users --

APBS 1.2.1 has been released.  This is a bugfix release specifically aimed at addressing a problem with certain nonlinear Poisson-Boltzmann calculations.  In particular, several users noticed that Poisson-Boltzmann calculations which focused into a low dielectric region would occasionally generate very large (~1E25 kJ/mol) energies.  This was due to a bug that caused instability in the nonlinear Poisson-Boltzmann solver.  This bug has been fixed in this release.

The full list of changes is:
    • Added in warning into focusFillBound if there is a large value detected in setting the boundary conditions during a focusing calculation
    • Added in a check and abort in Vpmg_qmEnergy if chopped values are detected. This occurs under certain conditions for NPBE calculations where focusing cuts into a low-dielectric regions.
    • Fixed a bug in Vpmg_MolIon that causes npbe based calculations to return very large energies.  This occurs under certain conditions for NPBE calculations where focusing cuts into a low-dielectric regions.

More information about APBS as well as download links can be obtained from http://www.poissonboltzmann.org/.

We apologize for this bug and thank you for your continued support of APBS.

Sincerely,

The APBS Development Team