[PyMOL] Ruge problem visualization of PDBQT file on pymol

[EDUARDO J. A. C. <ed...@ep...>]

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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