Article ID: 266 - Last Modified: August 19, 2014
Can I generate Glide grids with hydrophobic constraints from the command line, or via a Python script?
Hydrophobic constraints are no longer available, as of the 2014-3 release, and their generation in previous releases was not possible to script, because the hydrophobic constraint required an auxiliary .phob file containing details of the hydrophobic boxes generated in Maestro for a given receptor structure.
Instead, you should use positional constraints. During the docking job setup, you can specify the ligand feature to be Hydrophobic for this positional constraint. The relevant Grid Generation input file keywords for a positional constraint are:
where the *POS keywords indicate the coordinates of the center of the positional constraint, and the RPOS keyword indicates the radius of the positional constraint. You will need some mechanism for computing the appropriate coordinates for each receptor, but this can be done via a Python script (e.g., by calculating the centroid of certain residues common to all receptor structures). You also will need to increment GLIDE_NTOTALCONS and add a constraint label to GLIDE_CONSNAMES when you add the positional constraint.
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