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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