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
out_ZINC100199761-5_mJHBP1.pdbqt
Description: Binary data
ZINC100199761-5.pdbqt
Description: Binary data
ZINC100199761-5.mol2
Description: chemical/mol2
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