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

[Elaine Meng]

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>