[Chimera-users] Fatal error during Energy minimization

[Elaine Meng]

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