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Article ID: 561 - Last Modified: December 4, 2010

Is there way to automate the process of docking to a set of receptor conformations, which includes grid generation for each of them?

If you have just a few receptor structures, you can set up a Virtual Screening Workflow job that will dock a ligand set to multiple grids generated by the workflow. This does require you to set up the Grid Generation parameters for each receptor structure used.

Another option would be to use the XGlide cross-docking script from our website (xglide.py). This is a command-line script designed for cross-docking (i.e., given a set of complexes, generate grids for all and dock all the ligands into each receptor structure), but it can be used in other contexts. By specifying multiple RECEPTOR files in the input parameter file, plus the input LIGAND file, you could generate grids for the receptor conformations and then dock the ligands to each. This script does not combine all the docking results together the way VSW does, however; you could combine the individual docking results files from the jobname_workdir directory with $SCHRODINGER/utilities/glide_merge or $SCHRODINGER/utilities/glide_ensemble_merge.

If you are generating grids for an apo protein, the only way to specify the grid center in XGlide is to provide explicit coordinates via the GRIDGEN_GRID_CENTER keyword. If your active site coordinates are not aligned, you'll have to align the receptor structures first, either via the ALIGN option in XGlide, or by first superimposing the structures in Maestro.

Keywords: docking, grid generation, VSW, XGlide cross-docking script

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