[Chimera-users] SDF Partial Charges

[Eric Pettersen]

On Jan 31, 2010, at 3:32 PM, Nancy wrote:

> Hello,
>
> I am performing protein-ligand docking simulations, and the  
> preferred ligand input file format is Mol2.  I obtained some of my  
> ligand structures from PubChem in SDF format, and I noticed that the  
> SDF files contain partial charges  
> ("PUBCHEM_MMFF94_PARTIAL_CHARGES").  Is there a way to preserve the  
> charges in Chimera when converting to Mol2 file format?

Hi Nancy,
	I don't know if you are going to continue to use Chimera for your SDF- 
 >Mol2 conversion given my response to your other question, but  
Chimera doesn't handle the PubChem-only fields, no.  I wasn't aware  
they existed until your question!  Now that I know about them I think  
Chimera should handle them.  I will open an enhancement-request ticket  
in the Chimera Trac database for this feature.  In the interim, you  
would have to extract the charge from the SDF file yourself and write  
a "defattr" file to get them assigned as the "charge" attribute of  
each atom, as outlined here:

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/defattr.html

I've attached an SDF and corresponding defattr file.
	You could even do this after generating a Mol2 via OpenBabel (and  
reading that into Chimera) since Chimera will honor Mol2 atom/bond  
types that came from the input and will leave them unchanged on output.

--Eric

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


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