Protein Logand Docking

[R A J Rajkishore]

Hello All,

I am a newbie in docking (Protein-Ligand Docking in Autodock).
I have experience in doing Virtual Screening but I am stuck in the middle of my work.

It is , I have collected a protein PDB structure from PDB having ligand ISONIAZID binding to one of amino acid.
I want to separate the ligand and bind it once at the same position.

I have used Autodock for this.

Unfortunately am unable to bind the ligand at the same position earlier it was binded, rather, it is binding in different angle to that amino acid.

Please suggest me and help me.

With Regards