Re: [Open Babel] problem with incorrect assignment of bond order/carbocation status in pdb file

[Geoffrey H. <ge...@ge...>]

> I have attached a PDB format file, derived from the molecule tamiflu  
> in complex with neuraminidase with the following errors:

Try OB-2.2.1.

> I understand that much of this is inferred from the MMFF parameter  
> files, and may be problem specific to the PDB file. I think this  
> might be indicative of less than graceful behavior in the presence  
> of noisy position information, however.

This has nothing to do with MMFF94 or other force fields. Open Babel  
assigns bond order based on the geometry of the atoms after  
determining connectivity. Since there are no explicit hydrogens, it  
has to make some guesses. The two terminal ethyl groups have bond  
angles suspiciously close to 120 degrees.

In 2.2.1, I added a check for terminal atoms -- it won't assign triple  
or double bonds unless the bond length is reasonable for a multiple  
bond. In your case, C-C ~ 1.5Å, so it's clearly a single bond.

Cheers,
-Geoff