[Chimera-users] how to solve the problem of topology

[Kenji MATSUI]

Dear Elaine

Thank you for taking the time to reply.

I have been trying to do this after your email in February, but I could not
solve the problem as I wanted to.

I will ask the swiss dock and Gromacs people about it.

Thank you again for answering all of our questions.


---------------------------------------------------------------------------

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


2022年5月31日(火) 1:09 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji,
> This is the same question you asked back in February, please see previous
> e-mail chain:
>
> <
> https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018472.html
> >
> <
> https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018473.html
> >
> <
> https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018474.html
> >
> <
> https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018475.html
> >
> <
> https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018476.html
> >
>
> We never did completely answer you because we did not write that tutorial
> and I could not see any problems with your files.
>
> Maybe you can ask the Swissdock or Gromacs people for advice.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On May 29, 2022, at 5:55 PM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera
> >
> > Thank you for your support the other day.
> >
> > I also apologize for contacting you outside of business hours due to the
> time difference.
> >
> > Excuse me,  I have a question about the issue of ligand topology for the
> docking study.
> >
> > ligand: 25-hydroxy cholesterol
> >
> > The topology did not match when I used this ligand for the docking study.
> >
> > Could you tell me how to solve this problem?
> >
> > The thing I tried
> >
> > 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL
> below, but it did not work
> >
> > Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html
> >
> > 2.  I tried to change the conformation of the C23-24 part, but
> > the situation won't be changed.
> >
> > Reference:<
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
> >
> >
> >
> >
> ---------------------------------------------------------------------------
> > 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
> > <25-hydroxycholesterol(Osh4).pse>
>
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