[Chimera-users] Converting SDF to Mol2: Errors

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 1 15:55:19 PST 2010

On Jan 31, 2010, at 4:32 PM, Nancy wrote:

> Hi All,
> When I convert an SDF file to Mol2 format using UCSF Chimera, I  
> noticed that some valence errors were introduced.  I can correct  
> these errors for individual molecules, but doing so for large sets  
> becomes cumbersome; is there any solution to this problem?

Hi Nancy,
	When you say "valence errors" do you mean (1) outputting atom types  
that imply hydrogens not present in the structure, or (2) incorrect  
bond orders?
	If (1), Chimera does not assume that compounds/structures have all  
required hydrogens and therefore may output atom types that imply  
hydrogens that are not explicitly present.  If this is the issue I  
could add code to allow for outputting atoms types compatible with the  
structure "as is", but it would take me awhile to do that since it  
would be some work.  In the interim you might consider doing the SDF  
conversion using OpenBabel which I believe will output atom types  
consistent with your structure "as is".  One possible issue is that  
OpenBabel will include its own charges with the Mol2 file, regardless  
of MMFF charges in the SDF file (though it's possible you would prefer  
the OpenBabel charges).  If you are going to do this conversion in  
bulk you would probably want to get your own copy of OpenBabel  
running, but you could try some initial tests using these web servers:


	If (2), Chimera does remember the SDF bond orders it read in, but  
doesn't use the remembered values in Mol2 output.  SDF bond orders are  
not usually of much use for informing Mol2 bond orders, since there  
are no indicators of amide bonds, and aromatic bonds are typically  
indicated as alternating single and double bonds (despite the fact  
that there is an SDF value for indicating aromatic bonds).  Therefore  
I don't think you want to include SDF bond orders in Mol2 output.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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