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Article ID: 266 - Last Modified: December 4, 2010

Can I generate Glide grids with hydrophobic constraints from the command line, or via a Python script?

Unfortunately, it isn't possible to script the creation of a hydrophobic constraint for Grid Generation, because the hydrophobic constraint requires an auxiliary .phob file containing details of the hydrophobic boxes generated in Maestro for a given receptor structure.

One alternative would be to use a positional constraint instead of a hydrophobic constraint. 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

GLIDE_NUMPOSITCONS 1
GLIDE_CONS_XPOS 5.808778
GLIDE_CONS_YPOS 8.451618
GLIDE_CONS_ZPOS 22.075826
GLIDE_CONS_RPOS 3.000000

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.

Keywords: grid, generation, hydrophobic, constraint, script, command line

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