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