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

[Elaine Meng]

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>_______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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> 
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