[Dock-fans] Cannot find consistent set of bond orders

[Eric Pettersen]

> I m adding Hydrogen to my ligand file .Actually this file contain 1990
> ligand .Now while adding hydrogen ,this is givin chimera error :-
> Cannot find consistent set of bond orders for ring system containing  
> atom
> #0.1881:1.het at C
> Cannot find consistent set of bond orders for ring system containing  
> atom
> #0.1942:1.het at C
> so on ,....................
> what should i do to remove this error ? Pls reply me ...


Hi Shalu,
	For planar ring systems Chimera tries to determine the bond orders  
around the ring.  These messages mean that given the estimated atom  
types connected to or in the rings Chimera couldn't come up with a set  
of bond orders that worked for those rings.  This either means that  
the molecules are bad or that (more likely) Chimera mis-guessed some  
of the atom types involved in the rings.
	Nonetheless Chimera will protonate the molecules as best it can.   
What you should do is look at those particular molecules and verify  
that the protonation is what you expect.  If not, you will have to  
either use Actions->Atoms/Bonds->delete to delete (selected) excess  
hydrogens or use Tools->Structure Editing->Build Structure to add/ 
reposition hydrogens (via the Change Atom tab) on selected atoms.
	You might also consider sending me the ligands that Chimera is having  
problems with so that I can try to improve Chimera's handling of those  
moieties.

--Eric


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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