<div dir="ltr">Dear Elaine<div><br></div><div>Thank you for taking the time to reply.<br><br>I have been trying to do this after your email in February, but I could not solve the problem as I wanted to.<br><br>I will ask the swiss dock and Gromacs people about it.<br><br>Thank you again for answering all of our questions.<br><div><br></div><div><br><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><span style="color:rgb(34,34,34)">------------------------------</span><span style="color:rgb(34,34,34)">------------------------------</span><span style="color:rgb(34,34,34)">---------------</span></div><div><br></div><div><span style="color:rgb(34,34,34)">Kenji Matsui</span><br style="color:rgb(34,34,34)"><span style="color:rgb(34,34,34)"> Graduate School of Tokyo University of Agriculture and Technology　M2</span><br style="color:rgb(34,34,34)"><span style="color:rgb(34,34,34)">2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan</span><br style="color:rgb(34,34,34)"><div style="color:rgb(34,34,34)"> Mail: <a href="mailto:s214903z@st.go.tuat.ac.jp" style="color:rgb(17,85,204)" target="_blank">s214903z@st.go.tuat.ac.jp</a></div></div></div></div></div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2022年5月31日(火) 1:09 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Kenji,<br>
This is the same question you asked back in February, please see previous e-mail chain:<br>
<br>
<<a href="https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018472.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-February/018472.html</a>><br>
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<br>
We never did completely answer you because we did not write that tutorial and I could not see any problems with your files.<br>
<br>
Maybe you can ask the Swissdock or Gromacs people for advice.<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.                       <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On May 29, 2022, at 5:55 PM, Kenji MATSUI via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Dear Chimera<br>
> <br>
> Thank you for your support the other day.<br>
> <br>
> I also apologize for contacting you outside of business hours due to the time difference.<br>
> <br>
> Excuse me,  I have a question about the issue of ligand topology for the docking study.<br>
> <br>
> ligand: 25-hydroxy cholesterol<br>
> <br>
> The topology did not match when I used this ligand for the docking study.<br>
> <br>
> Could you tell me how to solve this problem?<br>
> <br>
> The thing I tried<br>
> <br>
> 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL below, but it did not work<br>
> <br>
> Reference: <a href="https://www.swissparam.ch/SwissParam_gromacs_tutorial.html" rel="noreferrer" target="_blank">https://www.swissparam.ch/SwissParam_gromacs_tutorial.html</a><br>
> <br>
> 2.  I tried to change the conformation of the C23-24 part, but <br>
> the situation won't be changed.  <br>
> <br>
> Reference:<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust</a>><br>
> <br>
>  <br>
> ---------------------------------------------------------------------------<br>
> Kenji Matsui<br>
>  Graduate School of Tokyo University of Agriculture and Technology　M2<br>
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan<br>
>  Mail: <a href="mailto:s214903z@st.go.tuat.ac.jp" target="_blank">s214903z@st.go.tuat.ac.jp</a><br>
> <25-hydroxycholesterol(Osh4).pse><br>
</blockquote></div>