I want to dock a series of compounds within a grid, then select the docked poses in the receptor and define them to be excluded volumes (as is possible in the Schrodinger Maestro GUI) and create new grids using these selections. From there, I will dock further molecules into the newly created grids with the excluded volumes.
Is this possible in KNIME? The settings for the Glide Grid Generation node seem somewhat limited and I’m unable to find another way to define excluded volumes.
Unfortunately there is no direct way to add excluded volumes through the Glide Grid generation panel and I haven’t found an easy way to add these using parameter flow variables either. It would be possible to do this using the Chemistry External Tool node and call the glide code directly but you would have identify of course the coordinates for the excluded volumes which could be possible using the Knime-Maestro Connector node.
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