how to solve the problem of topology
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
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
- 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
- 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@st.go.tuat.ac.jp <25-hydroxycholesterol(Osh4).pse>
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
- 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
- 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>
participants (2)
-
Elaine Meng
-
Kenji MATSUI