[Chimera-users] Fatal error during Energy minimization

[Saousen Diaf]

thank you Elaine, I will try with what you recommended.

best
Saousen

On Thu, Jun 2, 2022 at 11:15 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Saousen,
> The Antechamber charge calculation is meant to be easy for users, and to
> work for a large variety of molecules, but it does not work for
> everything.  It may be that the glycosylation group is simply too large for
> it to handle.  You could try using the simpler "Gasteiger" charge
> calculation method instead of the default semi-empirical "AM1-BCC" method.
>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
>
> It is usually not possible for us to give specific advice if we don't have
> your exact structure to try.  So when you get an error message that you
> think is a bug, instead of sending e-mail here you should use Chimera menu:
> Help... Report a Bug and attach the PDB file or a session file that has
> your structure in it (or at least some structure that generates the same
> problem) to the bug report.  You should include a brief written description
> of what happened, and your e-mail address if you would like a response.
>  The error message says "check reply log for details" and the bug report
> will include the reply log, whereas your email did not include those
> details.
>
> First try using Gasteiger as suggested above, and then if you still have a
> problem use Help... Report a Bug.  However, even if you do that, I cannot
> predict whether it will be possible to minimize your structure or not.
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 2, 2022, at 7:12 AM, Saousen Diaf via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear all,
> > I am using structure minimize tool in UCSF Chimera to minimize a
> glycosylated structure, but I get a fatal error:
> > Failure running ANTECHAMBER for residue BMA+MAN+NAG+MAN+NAG+PHE+MAN+ASN
> > Check reply log for details
> > any idea on how to resolve the issue.
> > Thank you in advance for your help.
> > Best
> > Saousen
>
>
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