> * with ./Typing.exe 10gs_ligand.sdf, the 4th atom is of type "o" (which is
> the good type)
> * with ./Typing.exe 10gs_ligand.xyz, the 4th atom is of type "os"
While I can't comment on the particular files, an XYZ file has no bonding
information whatsoever. While the bond perception in OB is fairly good, there's
no way that typing can be perfect when you've thrown away all the bonding
information.
So yes. Atom types for GAFF or other force fields will depend on the bonding
information, which depend on the file type.
Where possible, use file types like SDF or Mol2 that retain bonding information
if you want to retain atom typing.
-Geoff
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