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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