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Article ID: 610 - Last Modified: November 19, 2013

I have a complex, with the ligand and protein in separate PDB files, in the same coordinate frame. I'd like to make a grid file on the command line. Is there a way I can do so and specify the grid center using the ligand?

The input file for Glide Grid Generation jobs allows specification of the grid box center only by explicit X, Y, Z coordinates. So one option would be to determine the center coordinates yourself (say, with a Python script that computes the centroid of the ligand atoms) and then write the input file yourself, perhaps based on a template generated once by Maestro.

Another option would be to use the cross-docking script xglide.py from our website (Resources & Downloads → Scripts, in the Docking section). You can run this script with the command

$SCHRODINGER/run xglide.py myjob.in

The input file myjob.in would have to contain the following lines:

RECEPTOR myrecep.maegz
LIGAND mylig.maegz,myrecep.maegz,REFPOSE
GRIDGEN_GRID_CENTER SELF
SKIP_DOCKING TRUE

This will generate a Glide grid from the receptor and ligand files in the myjob_workdir directory. You would have to convert your PDB files to Maestro format with the utility pdbconvert, and it would be advisable to prepare the protein with the utility prepwizard.

Please note that it is not possible to set up constraints for grids using XGlide. For this, you'll have to use Maestro, write your own Glide Grid Generation input file by hand, or develop a Python script to create the input file.

Keywords: Glide grid, command line

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