[Dock-fans] ligand file input

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 16 17:27:18 PDT 2007


What I can say is that all the discrepancies favor the OpenBabel  
version, so you should use that.  I will work on making Chimera  
perform better here.  The discrepancies I can see are:

1) wrong bond orders between aromatic carbons and non-ring sp2 heavy  
atoms
2) failure to identify amide moiety
3) failure to use N.ar type for aromatic ring nitrogens

--Eric


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


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