Re: [Open Babel] Problem in converting a PDB file to MOL2

[Alexandre F. <ale...@gm...>]

Alexandre Fassio wrote
> 
> Geoff Hutchison wrote
>>> Indeed, we've tried the SDF and it is a good option. However, some small
>>> ligands have covalent bonds with other small ligands and by using the
>>> SDF
>>> format we won't able to detect it correctly.
>> 
>> Can you give us some concrete examples of what you mean?
>> 
>> -Geoff
>> 
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> Sure Geoff.
> 
> My first example is the Cellobiose (id CBI) that is a disaccharide.
> Sometimes, this ligand is found represented as two glucoses (GLC). If you
> want, you can see an example in the PDB 5A05
> (http://www.rcsb.org/pdb/explore/explore.do?structureId=5A05).
> 
> Another example is in attachment. This file was extracted from the PDB
> 1H4P and it has 8 ligands. 
> lig_example.pdb
> <http://forums.openbabel.org/file/n4659042/lig_example.pdb>  
> 
> If you open these examples in Pymol, for example, you'll see the ligands
> covalently bonded. 
> 
> In my work, I need to analyze the pharmacophore properties of the atoms.
> If I use the SDF of only one ligand I'll not consider the covalent bonds,
> thus this will not generate a properly analysis.
> 
> Thanks

Sorry, I made a mistake. The PDB 5A05 does not have a Cellobiose (CBI)
represented by two glucoses. Even so, this PDB has some examples of ligands
covalently bonded.



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