[Chimera-users] Question: How to do add charge and minimazation?

[Eric Pettersen]

Hi Kenji,
	The charge computation that Chimera carries out is actually performed by a separate program (antechamber, from AmberTools).  On Windows, as antechamber executes, that black window appears and will disappear when antechamber finishes.  The computation takes awhile on a molecule as big as the one you're using.  On my 2015 Mac it take 87 seconds to finish.  At any rate, the black window is nothing to worry about.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 9, 2023, at 6:38 PM, Kenji MATSUI via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear chimera
> 
> I am sorry to interrupt your busy schedule.
> 
> My name is Matsui, and I am a second-year master's student at a Japanese university.
> Thank you for taking time out of your busy schedule to respond to my question the other day.
> 
> We are investigating  interactions between protein and ligand.
> 
> I want to optimize the attached file compound. I want to adjust the charge for this purpose.
> 
> <image.png>
> 
> Question
> However, when I press OK in the first photo section, a black screen appears as in the second photo.In you tube and other videos, I was moved to the save etc. screen. Is the charge optimization done correctly here?
> 
> <image.png>
> 
> ---------------------------------------------------------------------------
> Kenji Matsui
>  Graduate School of Tokyo University of Agriculture and Technology　M2
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
>  Mail: s214903z at st.go.tuat.ac.jp <mailto:s214903z at st.go.tuat.ac.jp><OSW-1_inactive_analogue.mol2>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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