Re: [Open Babel] Gasteiger partial charges
Karteek, You could have found your answer by searching for Gasteiger at forums.openbabel.org. As it happened, there was a recent posting titled mol2 generation partial charges model just last week. In short, simply convert your molecule into mol2 format: obabel input.sdf -O output.mol2 Ling From: karthik kumar karthik3...@gmail.com To: openbabel-disc...@lists.sf.net Sent: Monday, September 23, 2013 11:28 PM Subject: [Open Babel] Gasteiger partial charges Dear users, I am a novice to this package. I am interested to calculate the gasteiger partial charges for my system. Can anyone give me an example reg. this. Can anyone help me in determining the charges. Thanks in advance Karteek Kumar -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Gasteiger partial charges and the -p option
Sorry, I meant to cc the list in. Quoting Noel O'Boyle baoille...@gmail.com on Wed, 23 Nov 2011 20:06:40 +0100: There seems to be a series of related issues. By the way, you should really email the list, so that people are aware you want something done about it. - Noel On 23 November 2011 19:33, Douglas Houston dhous...@staffmail.ed.ac.uk wrote: I just checked and it is. Do you think this bug is related to this post?: http://forums.openbabel.org/Wrong-gasteiger-atomic-partial-charges-BUG-tp4096059p4096059.html Quoting Noel O'Boyle baoille...@gmail.com on Mon, 21 Nov 2011 18:47:36 +0100: I don't know. Is the bug report still open? On 21 November 2011 17:21, Douglas Houston dhous...@staffmail.ed.ac.uk wrote: Can I just check whether this bug was fixed for new 2.3.1 release? I don't see a mention of it in the release notes ... Quoting Noel O'Boyle baoille...@gmail.com on Mon, 7 Mar 2011 17:23:07 +: Please go ahead - it's the only way to ensure that issues like this don't fall between the cracks... On 3 March 2011 10:50, Douglas Houston dhous...@staffmail.ed.ac.uk wrote: OK, just to follow up on this, if no-one has any objections I will submit a bug report. Quoting Mathias W. m.we...@uni-bonn.de: Yeah, thats because I'm stupid - I didn't recognize that all these numbers were recognized as text :-( 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: That's strange, if I sum everything in the charge column in your molecule_H.mol2 file, I get -9.0 ... Quoting Mathias W. m.we...@uni-bonn.de: Servus, I get both times over all charge zero (with ob-2.2.3) (molecule_H2.mol2 was produced with -h) 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug -- Mathias _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Mathias Weigt Institute of Pharmaceutical Chemistry University of Bonn An der Immenburg 4 53121 Bonn Germany Phone: +49/228/73-5240 -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Re: [Open Babel] Gasteiger partial charges and the -p option
I tried to do this but I get a 500 Internal Server Error when I try to use the 'Add new' link here: http://sourceforge.net/tracker/?atid=428740group_id=40728func=browse Quoting Noel O'Boyle baoille...@gmail.com: Please go ahead - it's the only way to ensure that issues like this don't fall between the cracks... On 3 March 2011 10:50, Douglas Houston dhous...@staffmail.ed.ac.uk wrote: OK, just to follow up on this, if no-one has any objections I will submit a bug report. Quoting Mathias W. m.we...@uni-bonn.de: Yeah, thats because I'm stupid - I didn't recognize that all these numbers were recognized as text :-( 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: That's strange, if I sum everything in the charge column in your molecule_H.mol2 file, I get -9.0 ... Quoting Mathias W. m.we...@uni-bonn.de: Servus, I get both times over all charge zero (with ob-2.2.3) (molecule_H2.mol2 was produced with -h) 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug -- Mathias _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Mathias Weigt Institute of Pharmaceutical Chemistry University of Bonn An der Immenburg 4 53121 Bonn Germany Phone: +49/228/73-5240 -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Gasteiger partial charges and the -p option
Please go ahead - it's the only way to ensure that issues like this don't fall between the cracks... On 3 March 2011 10:50, Douglas Houston dhous...@staffmail.ed.ac.uk wrote: OK, just to follow up on this, if no-one has any objections I will submit a bug report. Quoting Mathias W. m.we...@uni-bonn.de: Yeah, thats because I'm stupid - I didn't recognize that all these numbers were recognized as text :-( 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: That's strange, if I sum everything in the charge column in your molecule_H.mol2 file, I get -9.0 ... Quoting Mathias W. m.we...@uni-bonn.de: Servus, I get both times over all charge zero (with ob-2.2.3) (molecule_H2.mol2 was produced with -h) 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug -- Mathias _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Mathias Weigt Institute of Pharmaceutical Chemistry University of Bonn An der Immenburg 4 53121 Bonn Germany Phone: +49/228/73-5240 -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Gasteiger partial charges and the -p option
OK, just to follow up on this, if no-one has any objections I will submit a bug report. Quoting Mathias W. m.we...@uni-bonn.de: Yeah, thats because I'm stupid - I didn't recognize that all these numbers were recognized as text :-( 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: That's strange, if I sum everything in the charge column in your molecule_H.mol2 file, I get -9.0 ... Quoting Mathias W. m.we...@uni-bonn.de: Servus, I get both times over all charge zero (with ob-2.2.3) (molecule_H2.mol2 was produced with -h) 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug -- Mathias _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Mathias Weigt Institute of Pharmaceutical Chemistry University of Bonn An der Immenburg 4 53121 Bonn Germany Phone: +49/228/73-5240 -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Gasteiger partial charges and the -p option
Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug Quoting Douglas Houston dhous...@staffmail.ed.ac.uk: Hi, I have observed something curious about variations in the way OpenBabel assigns Gasteiger charges. For example, babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h produces a molecule with an overall charge that is essentially 0. However, the command babel -isdf molecule.sdf -omol2 molecule_H.mol2 -p 7.4 produces a molecule that has an overall charge of -9.0. Both output files have had the same number of hydrogens added. Is this what's supposed to happen? I have attached the input file for others to test. This seems to happen with both 2.2.3 and 2.3.0, cheers, Doug _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Gasteiger partial charges and the -p option
That's strange, if I sum everything in the charge column in your molecule_H.mol2 file, I get -9.0 ... Quoting Mathias W. m.we...@uni-bonn.de: Servus, I get both times over all charge zero (with ob-2.2.3) (molecule_H2.mol2 was produced with -h) 2010/12/3 Douglas Houston dhous...@staffmail.ed.ac.uk: Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug -- Mathias _ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
