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: http://wwmm-svc.ch.cam.ac.uk/wwmm/html/observer.html http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=OpenBabel 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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu