Article ID: 560 - Last Modified: November 19, 2013
I want to perform ensemble docking of 50 substrates, using the conformations (about 500) of an apo protein generated by molecular dynamics, with Desmond. How do I go about this?
You can use VSW to perform ensemble docking, but you can only add receptor structures one at a time to generate grids. If you generate the grids independently (with a script, for example), you can select them all in VSW in a single operation.
Rather than docking to all 500 conformations, you could try clustering them into a smaller set of representative structures. There is a Desmond trajectory clustering script available from our web site (Resources & Downloads → Scripts, in the Molecular Dynamics section) or via Scripts → Update in Maestro.
Another option would be to use the XGlide cross-docking script from our web site (xglide.py). This is a command-line script designed for cross-docking (i.e., given a set of complexes, generate grids for all complexes 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. Note that since you'll be 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 the active site coordinates drifted during the MD simulation, 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: trajectory clustering,ensemble docking, Glide, VSW, Desmond
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