[Chimera-users] Failure Running ANTECHAMBER

[Mailyn Terrado]

Hi Elaine,

I removed the BEF ligand from the structure. I encountered this error
message when trying to Minimize the structure.

I appreciate all the help.

Regards,
Mailyn

On Fri, Mar 5, 2021 at 3:09 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> As mentioned in the previous reply, the charge calculation may fail on
> highly charged structures (like phosphoesters).
>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
>
> Elaine
>
>
>
> > On Mar 5, 2021, at 1:00 PM, Mailyn Terrado <
> mailyn.terrado at rosalindfranklin.edu> wrote:
> >
> > Hi Elaine,
> >
> > Thank you for your reply. I will try to remove BeF3 and re-run.
> >
> > I also encountered the same error with a different protein structure
> with the ligand ANP (phosphoaminophosphonic acid-adenyl ester, Formula: C10
> H17 N6 O12 P3.
> >
> > Thank you for the help.
> >
> > Regards,
> > Mailyn
> >
> > Regards,
> > Mailyn
> >
> > On Fri, Mar 5, 2021 at 2:37 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 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.
> > Best,
> > Elaine
> > -----
> > 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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>
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