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
