pyridinium and MMFF94

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pyridinium and MMFF94

Paolo Tosco
Dear OpenBabel developers,

I noticed that obenergy, as of the current development version
downloaded through SVN (20 July 2010), fails to assign correct atom
types to pyridinium ion; namely, aromaticity is not perceived, and all
atoms are assigned aliphatic atom types (2 for carbon, 8 for nitrogen),
while all formal charges are set to zero. On the contrary, correct atom
typing is observed for pyridine.

Best regards,
Paolo Tosco

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Re: pyridinium and MMFF94

Geoffrey Hutchison-3
> downloaded through SVN (20 July 2010), fails to assign correct atom
> types to pyridinium ion; namely, aromaticity is not perceived, and all

In what form are you importing the molecule? SMILES? PDB? If there is no assigned formal charge to the pyridinium nitrogen, then there is no guaranteed method to ensure it is typed correctly.

Best regards,
-Geoff


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Re: pyridinium and MMFF94

Geoffrey Hutchison-3
> You are right, using a correct SMILES string type assignment is perfect. Are you aware of a 3D-coordinate format from which OpenBabel could be able to extract formal charge information in order to assign types properly while retaining 3D coordinates rather than rebuilding them as starting from a SMILES string?


I believe SDFile would work just fine.

Best regards,
-Geoff

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Prof. Geoffrey Hutchison
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University of Pittsburgh
http://hutchison.chem.pitt.edu/
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