Article ID: 651 - Last Modified: August 19, 2014
I am unable to dock my ligand using core constraints. I receive the error "Core centroid is beyond tolerance 1.000000 of grid box". What is wrong?
The "Core centroid is beyond tolerance..." error means that the reference core is too far from the center of the grid box. This error indicates that the reference molecule used to define the core was not pre-positioned in the active site; or, it could be that the centroid of the core atoms is simply a bit too far away from the grid center. The latter case could happen if the chosen core atoms are from one end of a long ligand molecule, or if the grid center was not very close to the ligand core. In these cases, you should be able to get the job to run by increasing the size of the inner bounding box that limits the volume which a ligand center can explore while docking. To increase this box size, you will have to rerun Grid Generation, and adjust the inner (green) box via the "Advanced Settings" on the Site tab.
If you are using the XGlide script, it can happen if XGlide's mechanism for splitting the input complex into a receptor and ligand chooses the wrong ligand-size molecule as the 'ligand', causing the grid to be centered somewhere other than expected. Try adding an explicit ligand molecule number to the COMPLEX line of the input file and rerun with that modification.
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