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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