The bond orders may not have been guessed correctly. I suggest you open the sdf in Avogadro (for example) and check the structure.
On Mon, 23 Aug 2021, 15:24 Kevin Skinner, <kevi...@umich.edu> wrote: > I used Open Babel to convert an XYZ file to an SDF file. Both contained > 27 atoms. After using confab, the outputs contain 28 atoms. I am not > familiar with SDF files, so do you have any suggestions as to where > something might be wrong? > > - Kevin > > On Mon, Aug 23, 2021 at 9:51 AM Noel O'Boyle <baoille...@gmail.com> wrote: > >> Which means that there is something wrong with your input. Or rather, >> your input is not what you think it is. Take a look at that atom in the SDF >> and see if you can figure it out. >> >> Regards, >> Noel >> >> On Wed, 18 Aug 2021 at 22:25, Kevin Skinner <kevi...@umich.edu> wrote: >> >>> Using an SDF file as the input did not correct the issue. >>> >>> - Kevin >>> >>> On Wed, Aug 18, 2021 at 5:17 PM Noel O'Boyle <baoille...@gmail.com> >>> wrote: >>> >>>> Ah OK. Try an sdf file, and then there will be no need for OB to guess >>>> anything. >>>> >>>> On Wed, 18 Aug 2021, 21:50 Kevin Skinner, <kevi...@umich.edu> wrote: >>>> >>>>> Hello, >>>>> >>>>> Thanks for the response. I already have all of the hydrogens that are >>>>> present in the structure. Confab is adding an extra hydrogen because it >>>>> thinks there should be one. Typically it does so in between, but over a >>>>> bond (like a triangle). Is there a sway to approach this? If not, then >>>>> would the sampling still be correct and I would just need to remove it >>>>> from >>>>> all of the structures? >>>>> >>>>> Thanks, >>>>> >>>>> Kevin >>>>> >>>>> On Wed, Aug 18, 2021 at 3:47 PM Noel O'Boyle <baoille...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi Kevin, >>>>>> >>>>>> Working as intended. The forcefields and QM calculations require >>>>>> explicit hydrogens to correctly calculate the energy. It's trivial to >>>>>> remove the H afterwards, but this would be a bit unusual so think it >>>>>> over. >>>>>> >>>>>> Regards, >>>>>> Noel >>>>>> >>>>>> On Wed, 18 Aug 2021 at 16:25, Kevin Skinner <kevi...@umich.edu> >>>>>> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I am using confab to generate conformers, but while doing so it adds >>>>>>> a hydrogen to the structure. I have used the iQMol optimizer, PM3, and >>>>>>> DFT >>>>>>> for the optimizations and all have the same issue. I have tried using >>>>>>> both >>>>>>> XYZ and MOL2 inputs. Is there a way to avoid this issue? >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Kevin >>>>>>> >>>>>> _______________________________________________ >>>>>>> OpenBabel-discuss mailing list >>>>>>> OpenBabel-discuss@lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>>>>>> >>>>>>
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