Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows

[S.L. C. <sl...@ya...>]

Hello Greg,

Multiple bonds from metal ions (Ca, Mg, etc.) are not unusual in the PDB. And from what I remember, it is not even consistent in the sense that metal ions do not always have multiple bonds.

Do forcefields have parameters for bonds involving metal ions? If not, perhaps you could simply disregard all bonds involving metal ions?

Ling



>________________________________
> From: Greg Landrum <gre...@gm...>
>To: "Rdk...@li..." <Rdk...@li...> 
>Cc: Roger Sayle <ro...@ne...> 
>Sent: Sunday, November 24, 2013 9:51 PM
>Subject: Re: [Rdkit-discuss] reading PDB file failed after reading sdf on	Windows
> 
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>On Mon, Nov 25, 2013 at 5:10 AM, Greg Landrum <gre...@gm...> wrote:
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> 
>>Another problem is that I cannot read pdbs containing metals (e.g. 1vj5)
>>> 
>>>Is there any workaround for that problem? I hope you can help me…
>>
>>
>>That bug is reproducible on linux as well. The normal solution to this would be to skip the sanitization step that causes the error, but unfortunately it seems that also causes the PDB parser to fail. I'll take a look at fixing it.
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>I've now fixed the problem with not being able to skip sanitization, but I am still stuck on this particular protein.
>1VJ5 has a Mg atom (#4333) with CONECT records to six other atoms. This leads to a valence on Mg that is higher than the RDKit normally accepts.
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>How should this type of situation be handled by the PDB parser?
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>The irony of a PDB file wth *too many* CONECT records is killing me. :-)
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>-greg
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