With pdb files we have to guess the bond orders. With sdf files, we don't. There shouldn't be any other difference.
On Fri, 18 Oct 2019, 18:52 David van der Spoel, <sp...@xray.bmc.uu.se> wrote: > Hi, > > it seems that the algorithm for determining bonds and atomtypes depends > on the input file, is that correct? > When I run > > obenergy -ff GAFF file.pdb > I get different bonds then when I run > obenergy -ff GAFF file.sdf > > Since the atomtyping is done based on smarts I wonder whether different > algorithms are used for generating smarts depending on the input file? > > Alternatively, tips for debugging this, where to look in the code, would > be appreciated. > > Cheers, > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > > > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel >
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