I hope the "show spheres" command represents the ligands better for you.
------------------------------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> 04/01/22, 04:31:07 pm On Wed, Dec 15, 2021 at 11:59 PM EDUARDO JOSÉ AZEVEDO CORREA < edua...@epamig.br> 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 > > > (37)9997-5771 > > (37)3271-4673 > > *www.epamig.br <http://www.epamig.br/>* > > *EPAMIG Pitangui* > Rodovia BR - MG352 Km35 Zona Rural > > Caixa Postal 43 > > CEP 35650-000 - Pitangui - MG > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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