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

[Kenji MATSUI]

Dear Chimera

Thank you for answering my question.

I see.

Thank you for taking your time.
---------------------------------------------------------------------------
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


2023年1月11日(水) 5:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> 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
> <OSW-1_inactive_analogue.mol2>
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