Does your pdb file have hydrogens? If not, even more guessing. Gaussian files have all the atoms at least.
On Fri, 18 Oct 2019, 19:54 David van der Spoel, <sp...@xray.bmc.uu.se> wrote: > Den 2019-10-18 kl. 20:37, skrev Noel O'Boyle: > > With pdb files we have to guess the bond orders. With sdf files, we > > don't. There shouldn't be any other difference. > > How about Gaussian log files? It works with those as well. > Somehow there bond orders are derived correctly as well although no such > information is extracted from the log files. > > > > On Fri, 18 Oct 2019, 18:52 David van der Spoel, <sp...@xray.bmc.uu.se > > <mailto: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 > > <mailto:OpenBabel-Devel@lists.sourceforge.net> > > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > > > -- > 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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