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
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