[Chimera-users] Small molecules and antechamber

Eric Pettersen pett at cgl.ucsf.edu
Mon Aug 2 14:05:26 PDT 2010

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 Pettersen
                         UCSF Computer Graphics Lab

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