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

[Kenji MATSUI]

Dear Elaine

Thank you for taking the time to answer my question.

I apologize for the lack of clarity in some of the expressions.

"did not work" means even if you add, docking with swiss dock did not work.

The error message: topology of the ligand is not correct.

[image: image.png]

I tried to contact swiss dock about this, but swiss dock didn't seem to be
accepting queries, so I couldn't figure it out. So, I tried to improve it
by referring to the URL I attached before.

https://www.swissparam.ch/SwissParam_gromacs_tutorial.html

Please check it.

I'll try the method you taught me. Thank you very much.

---------------------------------------------------------------------------
松井 健治
 東京農工大学大学院 工学府産業技術専攻 修士
〒184-8588 東京都小金井市中町2-24-16
 Mail: s214903z at st.go.tuat.ac.jp

Kenji Matsui
 Graduate School of Tokyo University of Agriculture and Technology
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
 Mail: s214903z at st.go.tuat.ac.jp


2022年2月17日(木) 1:40 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji,
> I do not see the problem or understand what you mean by "did not work"...
> You have one structure that is cholesterol.  The other two structures are
> 25-hydroxycholesterol, which is a different molecule than cholesterol, so
> of course it will not have the same topology.   One of the two structures
> of 25-hydroxycholesterol has hydrogens, the other does not, but the
> hydrogens appear to be correctly added.  If you add hydrogens of course it
> will change the topology because there are more atoms.
>
> Maybe you only meant that the conformation of the C24-C27 part is
> different?  I can see a rotational difference but it has nothing to do with
> the hydrogens. The conformation is that way before you add hydrogens and
> adding hydrogens did not change it.  You can rotate the bonds to change the
> conformation if you want, e.g. the C23-C24 bond.  How to rotate bonds in
> Chimera (menu: Tools.. Structure Editing... Adjust Torsions):
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
> >
>
> We did not write that tutorial so I cannot comment specifically on it.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Feb 16, 2022, at 12:32 AM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera
> >
> > Thank you very much for your kind answers.
> >
> > Sorry, I have a question about the issue of ligand topology for the
> docking study.
> >
> > 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. Compare with the contents of the Mol2 file for cholesterol that was
> correctly docked.
> >
> > 25-hydroxycho_only_0216
> > → original file
> >
> > 25-hydroxycho_only_0216_Chimera
> > →after adding H using UCSF Chimera
> >
> ---------------------------------------------------------------------------
> > 松井 健治
> >  東京農工大学大学院 工学府産業技術専攻 修士
> > 〒184-8588 東京都小金井市中町2-24-16
> >  Mail: s214903z at st.go.tuat.ac.jp
> >
> > Kenji Matsui
> >  Graduate School of Tokyo University of Agriculture and Technology
> > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
> >  Mail: s214903z at st.go.tuat.ac.jp
> >
> <cholesterol_only.mol2><25-hydroxycho_only_0216_Chimera.mol2><25-hydroxycho_only_0216.mol2>_______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
>
>
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