David,
have you tried to see if other bond-typed formats, like Mol2, give the same or
different
results?
I suspect the bond typing to play a role in this issue. In my experience with
SMARTS and
PDBs, I noticed that very often bond recognition failed, sometimes due to tiny
deviations
from ideal geometries, and sometimes for unknown reasons.
If your 'file.sdf' was generated from 'file.pdb', then could it be that
obenergy does not
perform the exact same automated perceptions obabel does when converting the
files.
My 2 cents,
S
On 10/18/19 10:26 AM, David van der Spoel 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,
--
Stefano Forli, PhD
Assistant Professor
Center for Computational Structural Biology
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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