Hi,
> > I tried to convert the ligand DDP from the format PDB to MOL2. This ligand > can be found in the PDB 1IL5. > > However, Open Babel was not able to detect the aromatic atoms correctly. > For > example, the nitrogen N1 was set as an amide (am) instead of aromatic (ar). > I suspect that convert a PDB directly to Mol2 is not a good idea. I've > realized that some ligands in a PDB format sometimes present some errors in > the atoms classification. Does anyone know if a PDB conversion is not > indicated? > The conversion from pdb to mol2 works, but as you saw, errors for bond types are quite frequent. Indeed, the pdb format doesn't store information about bond types, and the software need to guess the bond type from atoms distances and geometry - other people will talk about that point much better than me. And atoms positions is often not precise enough in crystal structure. If you absolutely need the conformation of the pdb structure, the correct atom / bond types, and checking manually is not indicated, the way I followed years ago was to mix information from the pdb structure (coordinates) with a validated structure (e.g. found on the ligand page) (i.e. atoms and bond types), after pairing the atoms from each file. I don't know if ligands mol2 files with the pdb coordinates is already available somewhere, but I don't think so (but I would have interest for that too :) But beware of incomplete ligands, ligands which comprise many residues (e.g. peptides or peptidomimetics), and ligands covalently linked to protein or complexed to a metal :) At the time I worked on that, the sdf file of the ligand, with coordinates of the pdb structure, was not available. But today this sdf is available and should be correctly formatted for bond types (I didn't check). Did you try the sdf --> mol2 conversion, or perhaps doesn't it fit for your project? Regards, Pascal
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