[Chimera-users] cobalt in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 25 08:53:15 PDT 2020

On Mar 24, 2020, at 8:02 PM, Ke Shyue-Chu <ke at gms.ndhu.edu.tw> wrote:

> Hi, Elaine,
> I am trying to minimize an edited structure, Tools -> Structure Editing -> Minimize Structure --- using all default parameters, however, the cofactor B12 has a cobalt atom and that gives me an error message “Failure running ANTECHAMBER for residue B12[non-Co]. May I ask how to solve this problem?
> Thank you. 
> Best regards,
> Sc ke

Hi Sc ke,
It is not the cobalt ion causing the problem. That message says that ANTECHAMBER charge calculation failed on the non-Co part of residue B12, which means all the rest of the atoms besides Co, which is handled separately. That residue is large and complex and has a phosphate, all factors that are more likely to cause a failure of the AM1-BCC charge calculation method. You may have to use the simpler charge calculation method "Gasteiger" as specified  in the Add Charge dialog.


(For next time, to ensure you get an answer please send Chimera questions to chimera-users at cgl.ucsf.edu, CC-d here, rather than my individual address.)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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