[Chimera-users] Minimization troubleshooting

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 19 09:39:39 PDT 2021

Hi Nicole,
	There are several possibilities, and without having your structure it's impossible to be sure, but one of the most frequent causes of this error is that two or more atoms are directly on top of one another -- which produces an infinite energy and that minimization cannot resolve.  You should examine you structure to see if this is the case and if it is then resolve it somehow, either by adjusting initial coordinates or by deleting atoms.
	If this doesn't seem to be the problem as far as you can determine, use Help→Report A Bug in Chimera to submit a bug report and attach your structure file and I will investigate and get back to you.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jul 19, 2021, at 7:47 AM, Nicole Ostrovsky via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I am trying to perform minimizations on some structures I'm examining and each time the minimization is done and I open the reply log, the gradient norm says "-nan" and it tells me that no atoms were updated. I wasn't able to find anything online about how to fix this, so I'm emailing to ask if anyone would know how to troubleshoot this. 
> Thank you.
> Nicole Ostrovsky
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