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

Elaine Meng meng at cgl.ucsf.edu
Mon May 30 09:09:46 PDT 2022

Hi Kenji,
This is the same question you asked back in February, please see previous e-mail chain:


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.
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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