ADL: How to make a flexible chain staying in the active pocket

Gavin Seddon home at gavsed.net
Thu Apr 2 03:07:40 PDT 2009


Jun-Wei wrote:
> Dear AutoDockers,
>  
> I'm trying to dock a ligand to a metalloenzyme containing zinc ion by AutoDock4. The zinc is in the active pocket of the protein. My ligand has a sidechain containing five C-C single bonds, which should be located in the active pocket theoretically.
>   The question: when checking the docking results, all the docked poses bind to the protein surface around the pocket, instead of binding into the zinc pocket with the five C-C single bonds. What should I do to get the sidechain into the pocket? Thanks in advance!
>  
>   The grid box is properly set around the pocket and different zinc parameters have been tried.
>
> Best wishes,
> Junwei Zhao
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>
>   
Have you placed the gridcenter inside pocket?


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