There is a small ligand (straight chain 6 carbon atoms) and I have a
modelled structure for the receptor and its a GPCR.
By some in vitro studies I know where the ligand should bind. As described
by many people in the adt vina manual, I generated the grid that has centre
close to the binding site and is extended enough so that it includes enough
search space. Along with that I kept these residues of the binding site as
flexible. Also, the ligand has flexible bonds.
Now, the problem is, the ligand never binds there but goes everywhere else.
Is there a method to direct the binding to these residues? I am curious why
ligand wouldn't bind at this site in any of the docking.
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In AutoDock Vina, I do not believe there is a function to "force" what you're describing. In AutoDock, you can create a covalent map and force it to bind to one macromolecule atom. Check the PDB file for residues that look incorrect (usually at the bottom - or with the highest integer) For example, my last PDB had GDP1998 which occupied the pocket I wanted to bind to. It is necessary to delete these atoms before attempting to run AutoDock/Vina.
Also, I don't believe this is the case, but you may be restricting the search space too much or have the exhaustive-level too low. Please look into both of these possibilities and report back if the issue persists.
Undergraduate Researcher at Drexel University, Class of 2018
My posts do not reflect the views or knowledge base of Drexel University nor are they affiliated with the university.