On Jul 28, 2010, at 8:03 AM, Jon Rumbley wrote:

I have several small organic molecules constructed in ChemDraw and converted
in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add
charges to. I was simply using the add charge menu commands and AM1-BCC and
assuming the structures would be read as nonstandard but antechamber reports
an error with residue ****. The error log has no real indication of what the
trouble might be. Are there additional steps I must take before assigning
charges? The structures already have hydrogens added. An example .mol2 file
is below:

Hi Jon,
Using the file you provided (and that I've attached) I get no error in Chimera 1.4.1 nor the 1.5 daily build (though the latter is much slower due to the newer version of AmberTools using sqm to compute charges rather than mopac).  Can you tell me what version of Chimera you're using and what platform you're running it on?  Thanks!

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu