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

Kenji MATSUI s214903z at st.go.tuat.ac.jp
Sun May 29 17:55:29 PDT 2022

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.


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
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