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

[Kenji MATSUI]

Dear Elaine Meng

Thank you very much for your detailed answer to the last question. I
understand. Thank you very much for your kind response.
---------------------------------------------------------------------------
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18日(金) 7:59 Elaine Meng <meng at cgl.ucsf.edu>:

> Sorry, we are not experts in Swissdock or Gromacs, so I couldn't say what
> the problem is.
>
> I don't see any problem with the mol2 files that you sent.  I don't think
> that the problem is that you need to rotate any bonds, since the structures
> already appear to be correct as far as I can tell.
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Feb 17, 2022, at 2:46 PM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > 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.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>_______________________________________________
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