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@st.go.tuat.ac.jp 2022年5月31日(火) 1:09 Elaine Meng <meng@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@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.h...
---------------------------------------------------------------------------
Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z@st.go.tuat.ac.jp <25-hydroxycholesterol(Osh4).pse>