The atom numbering can be different depending on where the molecule is
coming from (SMILES or SDF) and
whether implicit hydrogens have been added. I think when the origin of the
molecule is SMILES the atom numbers are just the numbers of atomic symbols
in the SMILES string. The atom numbers in your image seems to come from
somewhere else as they are not consecutive.
Hope this helps,
Igor
On Wed, Apr 8, 2015 at 6:48 AM, Gulzar Singh <gulzar.sing...@gmail.com>
wrote:
> Hi
> This structure 'OC(=O)CCCCCCC/C=C\C/C=C\C/C=C\CC'. I want to rotate its
> tortionals but I get error
>
> File: Test.sdf
> Commnand: obrotate 'OC(=O)CCCCCCC/C=C\C/C=C\C/C=C\CC' Test.sdf 9 7 5 3 60
> Error: obrotate: The atoms of the rotating bond must be bonded.
>
> 9 7 5 3 are torsional as seen in attachment
> What am I doing wrong?
>
> Thank You
>
>
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