Hello Sundar,
Without access to your sd file I cannot be sure. But it is likely that you
have a nitrogen with a valence exceeding 4. You may need to, e.g., change
the N=O form into [N+][O-]. You may take a look at some of the following
threads.
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg06450.html
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg06774.html
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg06796.html
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg06798.html
Ling
On Wed, Dec 13, 2017 at 12:15 PM, Sundar <jubilantsun...@gmail.com> wrote:
> Hi RDkit users,
>
> I encounter following sanitize issue while I was trying to load an SD file
> using
> Chem.SDMolSupplier('lig.sdf')
>
> Explicit valence for atom # 16 N, 4, is greater than permitted
> ERROR: Could not sanitize molecule ending on line 3145
>
> The molecule RDkit complains about has a charged N atom.
> How do I sanitize it to fix these errors without losing its charge and 3D
> coordinates?
> Or how to disregard all these errors and get all the molecules read with
> nothing missing?
>
> Thanks,
> Sundar
>
>
>
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