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@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>

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Kenji Matsui

 Graduate School of Tokyo University of Agriculture and Technology　M2
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan

 Mail: s214903z@st.go.tuat.ac.jp

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