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Orientations and grow steps may be filtered prior to scoring to discard those in which the molecule significantly overlaps receptor atoms. This feature is enabled with the bump_filter flag. At the time of construction of the bump filter, the amount of atom VDW overlap is defined with the bump_overlap parameter (see Grid). At the time of bump evaluation the number of allowed bumps is defined with the max_bump parameter. If score optimization is being performed, then a few number of bumps should be allowed, since the minimizer can recover from such clashes. In addition, a few bumps often indicate an orientation that interacts intimately with the site and often leads to a strongly favorable orientation after minimization.
NOTE: The following parameter definitions will use the format below:
parameter_name [default] (value): #description
In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.
Bump Filter Parameters
* bump_filter [yes] (yes, no): #Flag to perform bump filtering * bump_grid_prefix [grid] (string): #The prefix to the grid file containing the desired bump grid * max_bumps  (int): #The maximum allowed number of bumps for a molecule to pass #the filter