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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