Re: [Open Babel] Java API: Can't use OB anymore due to UnsatisfiedLinkError
Found the issue: I recently installed Avogadro which ships with a different version of openbabel-2.dll. Because Avogadro adds PATH information to System variables in contrast to OpenBabel which uses user variables for PATH, the openbabel-2.dll in Avogadro is picked up first. My solution is to manually add the path to the openbabel installation to System PATH BEFORE Avogadro. -- View this message in context: http://forums.openbabel.org/Java-API-Can-t-use-OB-anymore-due-to-UnsatisfiedLinkError-tp4657311p4657313.html Sent from the General discussion mailing list archive at Nabble.com. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Conformer searching
Hi all, I would like to generate conformers for molecules such as C2H6 and N2H4, is this possible? The bonds in these molecules are not being detected as rotatable bonds, why is this? Best wishes, Scott -- View this message in context: http://forums.openbabel.org/Conformer-searching-tp4657314.html Sent from the General discussion mailing list archive at Nabble.com. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
Hold on, what is to rotate in a C2 or N2 molecule? And what would be a conformation for a diatomic structure aside from the trivial one??? It's just two atoms (not including hydrogens) with a single bond between them or did I misunderstand the question completely? Igor On Thu, Mar 20, 2014 at 10:54 AM, scott_m wrote: > Hi all, > > I would like to generate conformers for molecules such as C2H6 and N2H4, is > this possible? The bonds in these molecules are not being detected as > rotatable bonds, why is this? > > Best wishes, > > Scott > > > > -- > View this message in context: > http://forums.openbabel.org/Conformer-searching-tp4657314.html > Sent from the General discussion mailing list archive at Nabble.com. > > > -- > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/13534_NeoTech > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
Ethane (C2H6) and hydrazine (N2H4) have distinct minima that are separated by rotational barriers. Depending on the input structure, a geometry optimization (for instance in DFT) will bring you to one of these minima. I am interested in generating such conformations in a systematic way. Best wishes. Scott On 20 March 2014 15:06, Igor Filippov wrote: > Hold on, what is to rotate in a C2 or N2 molecule? And what would be a > conformation for a diatomic structure aside from the trivial one??? > It's just two atoms (not including hydrogens) with a single bond between > them or did I misunderstand the question completely? > > Igor > > > On Thu, Mar 20, 2014 at 10:54 AM, scott_m wrote: > >> Hi all, >> >> I would like to generate conformers for molecules such as C2H6 and N2H4, >> is >> this possible? The bonds in these molecules are not being detected as >> rotatable bonds, why is this? >> >> Best wishes, >> >> Scott >> >> >> >> -- >> View this message in context: >> http://forums.openbabel.org/Conformer-searching-tp4657314.html >> Sent from the General discussion mailing list archive at Nabble.com. >> >> >> -- >> Learn Graph Databases - Download FREE O'Reilly Book >> "Graph Databases" is the definitive new guide to graph databases and their >> applications. Written by three acclaimed leaders in the field, >> this first edition is now available. Download your free book today! >> http://p.sf.net/sfu/13534_NeoTech >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
I don't think openbabel can do DFT or any kind of ab initio quantum chemistry. Regards, Igor On Thu, Mar 20, 2014 at 11:15 AM, Scott McKechnie wrote: > Ethane (C2H6) and hydrazine (N2H4) have distinct minima that are separated > by rotational barriers. Depending on the input structure, a geometry > optimization (for instance in DFT) will bring you to one of these minima. I > am interested in generating such conformations in a systematic way. > > Best wishes. > > Scott > > > On 20 March 2014 15:06, Igor Filippov wrote: > >> Hold on, what is to rotate in a C2 or N2 molecule? And what would be a >> conformation for a diatomic structure aside from the trivial one??? >> It's just two atoms (not including hydrogens) with a single bond between >> them or did I misunderstand the question completely? >> >> Igor >> >> >> On Thu, Mar 20, 2014 at 10:54 AM, scott_m wrote: >> >>> Hi all, >>> >>> I would like to generate conformers for molecules such as C2H6 and N2H4, >>> is >>> this possible? The bonds in these molecules are not being detected as >>> rotatable bonds, why is this? >>> >>> Best wishes, >>> >>> Scott >>> >>> >>> >>> -- >>> View this message in context: >>> http://forums.openbabel.org/Conformer-searching-tp4657314.html >>> Sent from the General discussion mailing list archive at Nabble.com. >>> >>> >>> -- >>> Learn Graph Databases - Download FREE O'Reilly Book >>> "Graph Databases" is the definitive new guide to graph databases and >>> their >>> applications. Written by three acclaimed leaders in the field, >>> this first edition is now available. Download your free book today! >>> http://p.sf.net/sfu/13534_NeoTech >>> ___ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >> >> > -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
Thanks Igor but that was just an example of how you could find the minima from input structures, I am interested in generating the conformers using openbabel. Best wishes, Scott On 20 March 2014 15:21, Igor Filippov wrote: > I don't think openbabel can do DFT or any kind of ab initio quantum > chemistry. > > Regards, > Igor > > > On Thu, Mar 20, 2014 at 11:15 AM, Scott McKechnie wrote: > >> Ethane (C2H6) and hydrazine (N2H4) have distinct minima that are >> separated by rotational barriers. Depending on the input structure, a >> geometry optimization (for instance in DFT) will bring you to one of these >> minima. I am interested in generating such conformations in a systematic >> way. >> >> Best wishes. >> >> Scott >> >> >> On 20 March 2014 15:06, Igor Filippov wrote: >> >>> Hold on, what is to rotate in a C2 or N2 molecule? And what would be a >>> conformation for a diatomic structure aside from the trivial one??? >>> It's just two atoms (not including hydrogens) with a single bond between >>> them or did I misunderstand the question completely? >>> >>> Igor >>> >>> >>> On Thu, Mar 20, 2014 at 10:54 AM, scott_m wrote: >>> Hi all, I would like to generate conformers for molecules such as C2H6 and N2H4, is this possible? The bonds in these molecules are not being detected as rotatable bonds, why is this? Best wishes, Scott -- View this message in context: http://forums.openbabel.org/Conformer-searching-tp4657314.html Sent from the General discussion mailing list archive at Nabble.com. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >> > -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
Hi, Thanks Igor but that was just an example of how you could find the minima > from input structures, I am interested in generating the conformers using > openbabel. > > What about http://openbabel.org/wiki/Obconformer for the command line tool or http://openbabel.org/dev-api/group__conformer.shtml if you want to customize. I didn't try it myself, though. Best regards, Pascal -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
They're the type of tools I'm looking for but they don't produce any conformers for N2H4 and C2H6. Thanks, Scott On 20 March 2014 15:49, Pascal Muller wrote: > Hi, > > > > > > Thanks Igor but that was just an example of how you could find the minima >> from input structures, I am interested in generating the conformers using >> openbabel. >> >> > What about > http://openbabel.org/wiki/Obconformer for the command line tool > or > http://openbabel.org/dev-api/group__conformer.shtml if you want to > customize. > > I didn't try it myself, though. > > Best regards, > Pascal > -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
