I have a ligand that contains Rhenium metal. Now I want to dock this ligand with a protein so while preparation of this metal-ligand shows the problem in Autodock and Schrodinger. So anyone has idea regarding the preparation of this metal ligand
Search the literature (e.g., PubMed) for papers that used AutoDock to dock ligands containing rhenium.
Atom parameters for Rhenium is not defined by default in AutoDock. You can define the parameters for Re following the description in this link: http://autodock.scripps.edu/resources/parameters/AD4.1_bound.dat/view. Then, again it needs to be standardized. Another option I would suggest is to replace Re in the ligand with some other element (e.g., Mn, which is in the same group) for which the parameter is already defined and standardized. You should get a close approximate result. If you remove the metal altogether, it might render the ligand geometry more flexible (as the coordination bonds will be lost) and produce undesirable results.
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