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From: Baker, N. <nat...@pn...> - 2020-09-25 02:05:29
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Hi All – This mailing list is shutting down and moving to MailChimp. Please subscribe to the MailChimp list at https://poissonboltzmann.us11.list-manage.com/subscribe?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0 Thank you, -- Nathan Baker http://pronoun.is/he Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab Department of Applied Mathematics — University of Washington https://www.linkedin.com/in/nathanandrewbaker/ |
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From: Nathan B. <nat...@gm...> - 2020-03-04 04:31:58
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Hi APBS & PDB2PQR users - We would appreciate your help testing a new cloud-based version of APBS and PDB2PQR at http://apbs-rest-test.westus2.cloudapp.azure.com. This version is intended to eventually replace the web-based APBS/PDB2PQR instance currently hosted by NBCR. The process of moving APBS/PDB2PQR to a cloud-based architecture has triggered a redesign of the interface. We would appreciate your feedback on both the functionality of the new cloud-based service as well as the new web interface. Please provide feedback to me directly (nat...@gm...<mailto:nat...@gm...>), via the pdb...@li...<mailto:pdb...@li...> or apb...@li...<mailto:apb...@li...> mailing lists, or through the GitHub Issues page (https://github.com/Electrostatics/apbs-pdb2pqr/issues). If you have not already signed up, please register your use of the software at http://eepurl.com/by4eQr. Thank you very much for your feedback and continued support of the APBS/PDB2PQR software. Sincerely, Nathan Baker |
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From: Jurrus, E. R <Eli...@pn...> - 2016-03-26 13:51:06
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Dear APBS and PDB2PQR users – We are pleased to announce the release of PDB2PQR 2.1 which is now available from http://www.poissonboltzmann.org/docs/downloads/. There are several improvements and fixes (outlined below) to this release of the software and we encourage all users to upgrade. Please see http://www.poissonboltzmann.org/news/comp_pdb2pqr_release_history/ for the complete release notes. Thank you for your continued support of APBS and PDB2PQR. Sincerely, The APBS/PDB2PQR development team Notable new features: The old Monte Carlo method has been replaced with graph cut. See http://arxiv.org/abs/1507.07021 (To use the original Monte Carlo method, see verion 2.0) NEW FEATURES * Added alternate method to do visualization using 3dmol. * Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/) * Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly. * Added a check before calculating pKa's for large interactions energies. BUG FIXES * Fixed broken links on APBS submission page. * Added some missing files to querystaus page results. * Fixed some pages to use the proper CSS file. * Better error message for --assign-only and HIS residues. * Fix PROPKA crash for unrecognized residue. * Debumping routines are now more consistent across platforms. This fixes pdb2pka not giving the same results on different platforms. CHANGES * Added fabric script used to build and test releases. * The networkx library is now required for pdb2pka. KNOWN BUGS * If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter. * Running ligands and PDB2PKA at the same time is not currently supported. * PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (ie ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM ( 60 titratable residues will use 480MB ). We are working to fix this. |
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From: Nathan B. <nat...@gm...> - 2016-01-09 03:44:18
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Dear APBS & PDB2PQR users -- You are receiving this message because you are still subscribed to the old APBS/PDB2PQR mailing lists. Please update your subscription to the new lists by visiting http://eepurl.com/by4eQr. Thank you for your continued support of APBS and PDB2PQR! Sincerely, The APBS & PDB2PQR Development Team ---------- Forwarded message --------- From: APBS & PDB2PQR Biomolecular Solvation Software < nat...@gm...> Date: Fri, Jan 8, 2016 at 7:41 PM Subject: APBS 1.4.2 now available To: Nathan <nat...@ic...> APBS 1.4.2 is now available View this email in your browser <http://us11.campaign-archive1.com/?u=a5808042b2b3ea90ee3603cd8&id=f32947e2b6&e=cbebd7d419> APBS 1.4.2 is now available ------------------------------ Dear APBS and PDB2PQR users: We are pleased to announce the release of APBS 1.4.2 which is now available on GitHub <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=9a1baad17f&e=cbebd7d419> and SourceForge <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=77d115c85f&e=cbebd7d419>. New features and bug fixes for this release are described below. The latest information about APBS and PDB2PQR can always be found at http://www.poissonboltzmann.org/ <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=ed8a78d648&e=cbebd7d419> . Thank you for your continued support of APBS! Sincerely, The APBS & PDB2PQR Development Team ------------------------------ New Features - Poisson-Boltzmann Semi-Analytical Method (PB-SAM) packaged and built with APBS - New Geometric flow API and improvements in speed (#235 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=b6e24daad1&e=cbebd7d419> ) - Support for BinaryDX file format (#216 <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=173ddd0bde&e=cbebd7d419> ) - SOR solver added for mg-auto input file option - DXMath improvements (#168 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=53e3362d88&e=cbebd7d419> , #216 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=012e20cdf4&e=cbebd7d419> ) - Test suite improvements - APBS build in Travis-CI - Geometric Flow tests added - Protein RNA tests enabled (#149 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=5d69d102ef&e=cbebd7d419> ) - Intermetiate result testing (#64 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=709a649568&e=cbebd7d419> ) - Example READMEs onverted to markdown and updated with latest results Bug Fixes - OpenMPI (mg-para) functionality restored (#190 <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=f6cfc353ba&e=cbebd7d419> ) - Fixed parsing PQR files that contained records other than *ATOM* and *HETATM* (#77 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=0c07b2c433&e=cbebd7d419> , #214 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=c3b3b00013&e=cbebd7d419> ) - Geometric Flow boundary indexing bug fixed - Build fixes: - Out of source CMake builds are again working - Python library may be built (#372 <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=6c35d8d775&e=cbebd7d419> ) - CentOS 5 binary builds for glibc compatibility - Pull requests merged - Removed irrelevant warning messages (#378 <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=eefca7cc05&e=cbebd7d419> ) Notes The following packages are treated as submodules in APBS: - Geometric Flow has been moved to its own repository <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=b7e0599ca8&e=cbebd7d419> - FETk has been cloned <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=13baff3b2b&e=cbebd7d419> so that we have could effect updates - PB-SAM lives here <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=bd09191b31&e=cbebd7d419> We have added a chat feature <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=31e3a5c86a&e=cbebd7d419> for users. This can also be found from the support tab on http://www.poissonboltzmann.org/ <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=68bc8771d1&e=cbebd7d419> . Known Bugs - Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that doth not support C++11. This is also an issue for CentOS 5 - BEM is temprarily disabled due to build issues - Geometric Flow build is currently broken on Windows using Visual Studio <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=fac3dbf2ae&e=cbebd7d419> *Copyright © 2016 APBS & PDB2PQR Biomolecular Solvation Software, All rights reserved.* You are receiving this email because you opted in when registering your use of the APBS/PDB2PQR software. *Our mailing address is:* APBS & PDB2PQR Biomolecular Solvation Software PO Box 999, MSID K7-20 c/o Nathan Baker Richland, WA 99352 Add us to your address book <http://poissonboltzmann.us11.list-manage.com/vcard?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0> Want to change how you receive these emails? You can update your preferences <http://poissonboltzmann.us11.list-manage1.com/profile?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0&e=cbebd7d419> or unsubscribe from this list <http://poissonboltzmann.us11.list-manage.com/unsubscribe?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0&e=cbebd7d419&c=f32947e2b6> |
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From: Nathan B. <nat...@gm...> - 2015-10-08 18:04:11
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Dear APBS & PDB2PQR users --
I apologize for the additional email but we are having difficulties porting
our mailing lists to MailChimp due to its safeguards against spam and
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Therefore, we'd like your help in signing up for this new list by filling
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Thank you for your help and please accept our apologies for the additional
step.
Sincerely,
The APBS & PDB2PQR Development Team
On Wed, Sep 16, 2015 at 6:42 AM, APBS & PDB2PQR Biomolecular Solvation
Software <nat...@gm...> wrote:
> Moving the APBS/PDB2PQR mailing lists to MailChimp! View this email in
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>
> Over the past few months, we have been migrating APBS/PDB2PQR resources
> from SourceForge to other sites such as GitHub (
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> In the next few days, we will be moving the APBS and PDB2PQR announcements
> mailing lists to MailChimp (http://www.mailchimp.com
> <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=985ae31007&e=5eda05f532>).
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> No action is required on your part. However, if you are curious about the
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> Thank you for your continuing support of APBS and PDB2PQR.
>
> Sincerely,
>
> The APBS & PDB2PQR Development Team
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From: Baker, N. <Nat...@pn...> - 2015-09-16 13:34:34
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Dear APBS & PDB2PQR users -- Over the past few months, we have been migrating APBS/PDB2PQR resources from SourceForge to other sites such as GitHub (https://github.com/Electrostatics). In the next few days, we will be moving the APBS and PDB2PQR announcements mailing lists to MailChimp (http://www.mailchimp.com). Once this migration is complete, we will be sending a message from the new mailing list requesting your feedback on possible replacements for the APBS and PDB2PQR user mailing lists (e.g., StackExchange, Slack, Google Groups, LinkedIn, etc.). No action is required on your part. However, if you are curious about the new mailing list, we'd appreciate your help testing our new APBS/PDB2PQR registration form at http://eepurl.com/by4eQr. Thank you for your continuing support of APBS and PDB2PQR. Sincerely, -- Nathan Baker Laboratory Fellow Computational and Statistical Analytics Division Pacific Northwest National Laboratory +1-509-375-3997 https://goo.gl/H3X8f1 |
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From: Baker, N. <Nat...@pn...> - 2014-12-28 11:28:42
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Dear APBS and PDB2PQR users - We are pleased to announce the release of PDB2PQR 2.0 which is now available from http://www.poissonboltzmann.org/docs/downloads/. There are several improvements and fixes (outlined below) to this release of the software and we encourage all users to upgrade. Please see http://www.poissonboltzmann.org/pdb2pqr/release-history for the complete release notes. Thank you for your continued support of APBS and PDB2PQR. Sincerely, The APBS/PDB2PQR development team Notable new features: PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. Improved web interface. NEW FEATURES * Improved look of web interface * Option to automatically drop water from pdb file before processing. * Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA. * Support for compiling with VS2008 in Windows. * Option to build with debug headers. * PDB2PKA now detects and reports non Henderson-Hasselbalch behavior. * PDB2PKA can be instructed whether or not to start from scratch with --pdb2pka-resume * Can now specify output directory for PDB2PKA. * Improved error regarding backbone in some cases. * Changed time format on querystatus page * Improved error catching on web interface. BUG FIXES * Fixed executable name when creating binaries for Unix based operating systems. * Fixed potential crash when using --clean with extensions. * Fixed MAXATOMS display on server home page. * PDB2PKA now mostly respects the --verbose setting. * Fixed how hydrogens are added by PDB2PKA for state changes in some cases. * Fixed psize error check. * Will now build properly without ligand support if numpy is not installed. * Removed old automake build files from all tests ported to scons. * Fixed broken opal backend. CHANGES * Command line interface to PROPKA changed to accommodate PDB2PKA. PROPKA is now used with --ph-calc-method=propka. --with-ph now defaults to 7.0 and is only required if a different pH value is required. * --ph-calc-method to select optional method to calculate pH values used to protonate titratable residues. Possible options are "propka" and "pdb2pka". * Dropped support for compilation with mingw. Building on Windows now requires VS 2008 installed in the default location. * Updated included Scons to 2.3.3 * PDB2PKA can now be run directly (not integrated in PDB2PQR) with pka.py. Arguments are and . * No longer providing 32-bit binary builds. PDB2PKA support is too memory intensive to make this practical in many cases. KNOWN BUGS * If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter. * Running ligands and PDB2PKA at the same time is not currently supported. * PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (ie ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM ( 60 titratable residues will use 480MB ). We are working to fix this. |
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From: Nathan B. <nat...@gm...> - 2014-03-27 13:47:27
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Dear PDB2PQR users -- We are excited to announce the release of PDB2PQR 1.9. Details of this release are provided below. As usual, you can download the release from http://www.poissonboltzmann.org/pdb2pqr/d or start using it immediately via the web at http://nbcr-222.ucsd.edu/pdb2pqr. I would like to extend a special thanks to Kyle Monson and Nadya Williams for their hard work in getting this release ready. Thank you for your continued support of APBS and PDB2PQR. Sincerely, The APBS/PDB2PQR Development Team PDB2PQR 1.9.0 Notable new features: Binary builds. Binary builds do not require python or numpy be installed to use. Everything needed to run PDB2PQR is included. Just unpack and use. OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit. Linux binaries require CentOS 6 or newer and have been tested on Ubuntu 12.04 LTS and Linux Mint 13. If you are running 64-bit Linux use the 64-bit libraries. In some cases the needed 32-bit system libraries will not be installed on a 64-bit system. Windows binaries are 32 bit and were built and tested on Windows 7 64-bit but should work on Windows XP, Vista, and 8 both 32 and 64-bit systems. Windows support PDB2PQR can now be compiled and run on Windows using MinGW32. See http://mingw.org/ for details. Compilation with Scons PDB2PQR now uses Scons for compilations. With this comes improved automated testing. Please see http://www.poissonboltzmann.org/pdb2pqr/release-history for the complete release history NEW FEATURES - A ligand file with duplicate atoms will cause pdb2pqr to stop instead of issue a warning. Trust us, this is a feature, not a bug! - Improved error reporting. - Added support for reference command line option for PROPKA. - Added newresinter plugin to provide alternate methods for calculating interaction energies between residues. - Mol2 file handling is now case insensitive with atom names. - PROPKA with a pH of 7 is now specified by default on the web service. - Compilation is now done with scons. - Verbose output now includes information on all patches applied during a run. - Added stderr and stdout to web error page. - Added warning to water optimization when other water is ignored. - Command line used to generate a pqr is now duplicated in the comments of the output. - Added support for NUMMDL in parser. - Added complete commandline feature test. Use complete-test target. - Added propka support for phosphorous sp3. - Thanks to Dr. Stefan Henrich - Added a PyInstaller spec file. Standalone pdb2pqr builds are now possible. BUG FIXES - Rolled back change that prevented plugins from interfering with each other. Large proteins would cause a stack overflow when trying to do a deep copy. - Updated INSTALL file to reflect no more need for Fortran. - Fixed apbs input file to match what web interface produces. - Fixed user specified mobile ion species not being passed to apbs input file. - Removed ambiguous A, ADE, C, CYT, G, GUA, T, THY, U, URA as possible residue names. - Removed eval from pdb parsing routines. - Updated web links to refer to http://www.poissonboltzmann.org where appropriate. - Fixed hbond extension output to include insertion code in residue name. - Fixed debumping routines not including water in their checks. Fixes bad debump of ASN B 20 in 1gm9 when run with pH 7.0. - Fixed debumping failing to use best angle for a specific dihedral angle when no tested angles are without conflict. - Fixed debumping using asymmetrical cutoffs and too large cutoffs in many checks involving hydrogen. - Fixed debumping accumulating rounding error while checking angles. - Fixed inconsistencies in pdb parsing. - Thanks to Dr. Stefan Henrich - Fixed problems with propka handling of aromatic carbon/nitrogen. - Thanks to Dr. Stefan Henrich - Fixed case where certain apbs compile options would break web visualization. - Fixed improper handling of paths with a '.' or filenames with more than one '.' in them. CHANGES - Removed numpy from contrib. The user is expected to have numpy installed and available to python at configuration. - Support for numeric dropped. KNOWN BUGS - If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter. |
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From: Mahesh H. <ma...@bi...> - 2013-07-11 11:58:53
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hi, why some cases it comes like "WARNING: Unable to debump ALA A 43" ? please tell me the solution -- Sincerely, Mahesh Hegde -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. |
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From: Baker, N. <Nat...@pn...> - 2012-05-22 13:12:17
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Dear PDB2PQR community - I am in the process of writing a renewal proposal for the grant that supports APBS and PDB2PQR development. The impact of these software packages on the user community is an important evaluation criterion for such funding. Therefore, I would very much appreciate if you would be willing to provide examples of how APBS and/or PDB2PQR have played major roles in your research or teaching. Examples that emphasize the critical or unique roles of these packages are particularly important. Any feedback you can provide by Jun 10 would be much appreciated. Thank you for your help and your continued support of APBS and PDB2PQR! __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me<http://nabaker.me/> |
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From: Yingzhe L. <yin...@gm...> - 2012-03-01 02:05:43
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Dear all, recently, I have calculated the binding free energy between a protein and a ligand employing MM-PBSA method. The salvation energy was obtained from APBS. However, I want to the contribution of some key residues to binding free energy, what to setup in APBS? Any information would be appreciated! Best, yingzhe -- Yingzhe Liu Ph.D. Student of Analytical Chemistry Chemistry Department, Nankai University Tianjin, P.R.China, 30071 Tel: +86-022-23509425 Web: http://chinfo.nankai.edu.cn/ |
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From: Baker, N. <Nat...@pn...> - 2012-01-26 13:08:49
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Dear PDB2PQR users - 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<http://www.poissonboltzmann.org/pdb2pqr/release-history/version-1-8>. 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 __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://nabaker.me |
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From: Baker, N. <Nat...@pn...> - 2012-01-11 17:22:33
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Dear APBS & PDB2PQR Users - It has come to my attention that some of your e-mails have not reached me due to firewall configuration issues. Please address future inquiries to my Gmail address (nat...@gm...<mailto:nat...@gm...>) and/or the APBS/PDB2PQR user mailing lists. Thank you, Nathan Baker __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://nabaker.me |
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From: Baker, N. <Nat...@pn...> - 2011-09-16 13:53:45
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Hello -- As part of the aftermath of the California blackouts, the PDB2PQR server http://kryptonite.nbcr.net/pdb2pqr/ is current inoperable due to a hardware failure. We hope that this service will be back online as soon as possible. Thank you for your patience. Sincerely, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm |
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From: Baker, N. <Nat...@pn...> - 2011-09-13 16:33:49
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Dear PDB2PQR users -- We are pleased to announce the release of PDB2PQR 1.7.1a. This release contains bug fixes which are described in detail at http://goo.gl/QOaaQ. Among these changes are several important fixes which should be of broad interest to the community. * Added a force field example. * Fixed ligand command line option. * Fixed small bug in PQR output. * Fixed several errors in the web interface. * Updates to examples and documentation. 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 __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm |
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From: Baker, N. <Nat...@pn...> - 2011-04-03 00:06:55
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Dear APBS and PDB2PQR users -- This is a last reminder about the APBS/PDB2PQR survey which can be accessed at http://tinyurl.com/apbs-survey. Please be sure to respond before the survey closes on May 1 and enter for a chance to win a $25 Amazon.com gift certificate! Thank you for your support, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://signatures.pnl.gov > -----Original Message----- > From: Baker, Nathan > Sent: Wednesday, March 02, 2011 2:20 PM > To: Baker, Nathan > Subject: New APBS & PDB2PQR survey available > > Dear APBS and PDB2PQR users - > > Thank you very much for your continuing interest in and support of > APBS/PDB2PQR. As you know, we take user feedback very seriously and have > created an annual user survey to receive more widespread input into the > project. > > The survey can be accessed at: > > http://tinyurl.com/apbs-survey > > Please take a few minutes to complete this survey; 5 randomly-selected > participants will be awarded $25 Amazon.com gift certificates. This > survey will close on May 1. > > Thank you for your help! > > Sincerely, > > Nathan Baker > > __________________________________________________ > Nathan Baker > Chief Scientist for Signature Science > Pacific Northwest National Laboratory > 902 Battelle Boulevard > P.O. Box 999, MSIN K7-28 > Richland, WA 99352 USA > Tel: 509-375-3997 > nat...@pn... > http://signatures.pnl.gov |
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From: Baker, N. <Nat...@pn...> - 2011-03-02 22:20:14
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Dear APBS and PDB2PQR users - Thank you very much for your continuing interest in and support of APBS/PDB2PQR. As you know, we take user feedback very seriously and have created an annual user survey to receive more widespread input into the project. The survey can be accessed at: http://tinyurl.com/apbs-survey Please take a few minutes to complete this survey; 5 randomly-selected participants will be awarded $25 Amazon.com gift certificates. This survey will close on May 1. Thank you for your help! Sincerely, Nathan Baker __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... http://signatures.pnl.gov |
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From: Baker, N. <Nat...@pn...> - 2010-10-13 16:38:25
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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. * For PDB2PQR command-line and custom web interface users: the Opal service URLs have changed to new NBCR addresses. Old services hosted at *.wustl.edu addresses have been decommissioned. Please upgrade ASAP to use the new web service. Thank you as always to the staff at NBCR for their continuing support of APBS/PDB2PQR web servers and services. You can learn more about the latest version of PDB2PQR at http://www.poissonboltzmann.org/pdb2pqr. Access to the web interface and to downloads can be found at http://www.poissonboltzmann.org/pdb2pqr/d. Thank you for your continuing support of PDB2PQR. Sincerely, The PDB2PQR Development Team __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... www.pnl.gov |
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From: Nathan B. <ba...@bi...> - 2010-04-07 21:27:25
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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. Sincerely, Nathan Baker - 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 from inputgen.py and inputgen_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 in usage.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 of psize.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. -- Nathan Baker (http://www.nabgroup.org) Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis |
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From: Nathan <nat...@gm...> - 2009-11-06 12:41:05
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Hi All -- Please see the attached article which reports very sad news about the passing of Warren DeLano, creator of PyMOL. -- Nathan Sent to you by Nathan via Google Reader: In Memoriam: Warren L. DeLano via MacResearch - Online Community and Resource for Mac OS X in Science by dgohara on 11/5/09 It's with sadness that I bring the news that Warren L. DeLano passed away, suddenly and unexpectedly, on Tuesday November 3rd. For some of you, Warren's name will be instantly recognized. For many more, you know him indirectly as the developer of PyMOL. PyMOL, the open source software he began developing as a graduate student, would eventually become his life's work and has become one of the key tools used by structural biologists the world over. read more Things you can do from here: Subscribe to MacResearch - Online Community and Resource for Mac OS X in Science using Google Reader Get started using Google Reader to easily keep up with all your favorite sites |
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From: Nathan B. <ba...@bi...> - 2009-10-29 00:54:59
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Hi All -- (I am cross-posting this to the APBS-ANNOUNCE list because this release marks the availability of robust web-based APBS calculations.) We are pleased to announce the latest release of PDB2PQR, version 1.5, available for web-based use or download from http://www.poissonboltzmann.org/pdb2pqr . This version features a number of changes which are summarized online (http://tinyurl.com/pdb2pqr-1-5). Highlights include: * Web-based APBS execution * JMol-based web visualization of PDB2PQR and APBS potential calculations * Compressed APBS OpenDX output files in zip format, so that users can download APBS calculation zip files from the web server This release also marks the introduction of our new website for PDB2PQR at http://www.poissonboltzmann.org/pdb2pqr. Please let us know if you have any questions or concerns about PDB2PQR and thank you for your continued support of PDB2PQR. Sincerely, The PDB2PQR Development Team — Nathan Baker (ba...@bi...) Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis Web: http://bakergroup.wustl.edu/ |
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From: Nathan B. <ba...@bi...> - 2009-08-25 15:31:45
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Dear APBS and PDB2PQR users -- We would like to invite you to participate in a survey to evaluate the PDB2PQR and APBS software packages. Your participation will help prioritize our development efforts and will improve the functionality and performance of this software. The survey should take 10-15 minutes to complete. As an added incentive, $20 Amazon.com gift certificates will be awarded to 15 randomly-selected participants. The survey is available online: http://www.zoomerang.com/Survey/?p=WEB229K5XVXXAB Thank you for your help in improving APBS and PDB2PQR. Sincerely, Nathan Baker — Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis Web: http://bakergroup.wustl.edu/ |
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From: Nathan B. <ba...@bi...> - 2009-04-03 17:20:13
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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). Thank you for your continuing support of PDB2PQR. Sincerely, The PDB2PQR Development Team - NEW FEATURES * Updated html/master-index.html, deleted html/index.php. * Updated pydoc by running genpydoc.sh. * Added a whitespace option by by putting whitespaces between atom name and residue name, between x and y, and between y and z. * Added radius for Chlorine in ligff.py. * Added PEOEPB forcefield, data provided by Paul Czodrowski. * Updated inputgen.py to write out the electrostatic potential for APBS input file. * Updated CHARMM.DAT with two sets of phosphoserine parameters. * Allowed amino acid chains with only one residue, using --assign-only option. * Updated server.py.in so that the ligand option is also recorded in usage.txt. * Updated HE21, HE22 coordinates in GLN according to the results from AMBER Leap program. * Updated Makefile.am with Manuel Prinz's patch (removed distclean2 and appended its contents to distclean-local). * Updated configure.ac, pdb2pqr-opal.py; added AppService_client.py and AppService_types.py with Samir Unni's changes, which fixed earlier problems in invoking Opal services. * Applied two patches from Manuel Prinz to pdb2pka/pMC_mult.h and pdb2pka/ligand_topology.py. * Updated PARSE.DAT with the source of parameters. * Created a contrib folder with numpy-1.1.0 package. PDB2PQR will install numpy by default unless any of the following conditions is met: a. Working version of NumPy dectected by autoconf. b. User requests no installation with --disable-pdb2pka option. c. User specifies external NumPy installation. * Merged Samir Unni's branch. Now PDB2PQR Opal and APBS Opal services are available (through --with-opal and/or --with-apbs, --with-apbs-opal options at configure stage). * Added error handling for residue name longer than 4 characters. * Updated hbond.py with Mike Bradley's definitions for ANGLE_CUTOFF and DIST_CUTOFF by default. * Removed PyXML-0.8.4, which is not required for ZSI installation. * Updated propka error message for make adv-test -- propka requires a version of Fortran compiler. * Updated na.py and PATCHES.xml so that PDB2PQR handles three lettered RNA residue names (ADE, CYT, GUA, THY, and URA) as well. * Updated NA.xml with HO2' added as an alternative name for H2'', and H5" added as an alternative name for H5''. * Updated version numbers in html/ and doc/pydoc/ . * Updated web server. When selecting user-defined forcefield file from the web server, users should also provide .names file. * Removed http://enzyme.ucd.ie/Services/pdb2pqr/ from web server list. * Eliminated the need for protein when processing other types (ligands, nucleic acids). * Updated psize.py with Robert Konecny's patch to fix inconsistent assignment of fine grid numbers in some (very) rare cases. * Made whitespace option available for both command line and web server versions. * Updated inputgen_pKa.py with the latest version. -BUG FIXES * Fixed a legacy bug with the web server (web server doesn't like ligand files generated on Windows or old Mac OS platforms). * Fixed a bug in configure.ac, so that PDB2PQR no longer checks for Numpy.pth at configure stage. * Updated pdb2pka/substruct/Makefile.am. * Fixed isBackbone bug in definitions.py. * Fixed a bug for Carboxylic residues in hydrogens.py. * Fixed a bug in routines.py, which caused hydrogens added in LEU and ILE in eclipsed conformation rather than staggered. * Fixed a bug in configure.ac, now it is OK to configure with double slashes in the prefix path, e.g., --prefix=/foo/bar//another/path . * Fixed a bug in nucleic acid naming scheme. * Fixed a bug involving MET, GLY as NTERM, CTERM with --ffout option. * Fixed a bug for PRO as C-terminus with PARSE forcefield. * Fixed a bug for ND1 in HIS as hacceptor. * Fixed the --clean option bug. * Fixed a bug in CHARMM naming scheme. * Fixed a bug in test.cpp of the simple test (which is related to recent modifications of 1AFS in Protein Data Bank). -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
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From: Nathan B. <ba...@cc...> - 2008-01-06 03:02:30
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I apologize that the previous e-mail did not contain the download link: http://agave.wustl.edu/pdb2pqr/register.html On Jan 5, 2008 8:59 PM, Nathan Baker <ba...@cc...> wrote: > 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/ > > > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
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