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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