[Chimera-users] cobalt in Chimera

[Elaine Meng]

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.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>

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