[Chimera-users] Failure Running ANTECHAMBER

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 5 12:37:43 PST 2021

Hello Mailyn,
Probably the charge calculation step (Antechamber) cannot handle BeF3, sorry.  From the Add Charge manual page

"Note that Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules. GAFF allows for parametrization of most organic molecules made of C, N, O, H, S, P, F, Cl, Br and I."

As you know, BEF contains another element not in that list, Be.  You may be able to minimize if you delete the BEF residue first, but I don't know if that would be useful for your project.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. in general when you get an error message, you should not e-mail this help list but instead use Chimera menu: Help... Report a Bug, and in the bug report attach your session so that we can try your exact structure, include a short description of what you did, and also your e-mail address if you are hoping for a response

> On Mar 5, 2021, at 12:18 PM, Mailyn Terrado <mailyn.terrado at rosalindfranklin.edu> wrote:
> To whom it may concern:
> I am trying to use Chimera for protein Energy Minimization. I encountered a problem in running the program. Please find the attached screenshots of the error details.  The problem seemed to be with the ligand BEF (beryllium trifluoride).
> Any help would be greatly appreciated.
> Many thanks,
> Mailyn
> <Screenshot at 2021-02-26 15-53-49.png><Screenshot at 2021-02-26 15-55-21.png><Screenshot at 2021-02-26 15-55-46.png>

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