Re: [PyMOL] Ruge problem visualization of PDBQT file on pymol

[Saurabh G. <sau...@gm...>]

I hope the "show spheres" command represents the ligands better for you.

------------------------------

*Saurabh Gayali* / Post Doctoral Fellow
sau...@gm... / +91 8800412916

*CSIR-IGIB*
<http://example.com/>New Delhi, India

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04/01/22,
04:31:07 pm

On Wed, Dec 15, 2021 at 11:59 PM EDUARDO JOSÉ AZEVEDO CORREA <
ed...@ep...> wrote:

> Dear friends
> how are you? I hope you are doing well
> I am using autodock vina for virtual screening.. I used the LigPret to
> prepare my ligands into mol2 file, however when MGLTools convert the mol2
> to PDBQT and specially the vina output file in PDBQT has become a very
> anomalous and strange molecule structure.
> This file attached is ZINC100199761 molecule structure in mol2 generated
> from SMILE sequence using LigPrep. After LigPrep I pass it
> through the Avogadro to obtain the best geometry optimization
> Only after that I make the PDBQT conversion using the MGLTools and so the
> molecular docking using vina.
>
> Well did you know what is happening?? Is it a pymol visualization problem
> with pdqbt files?
> Could Anyone could know what the problem is and how to fix it?
> Thanks a lot!!
>
> have a nice end year
>
> Kinds Regards
>
> Eduardo Jose Azevedo Correa
> from Brazil
> --
>
> *Eduardo José Azevedo Corrêa*
>
> Biólogo| Professor e Pesquisador
>
>
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>
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>
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