Parameter Table

keyword	variable name	allowed values	default
contact_minimum	minscr	real	0.0
energy_maximum	maxscr	real	100.0
rmsd_override	usrdev	real	0.0

Parameter Descriptions

contact_minimum

provides the minimum contact score a ligand orientation must have in order to be written out during a SINGLE mode run. This variable is useful for reducing the number of low-scoring (and often uninteresting) orientations that are written out. The appropriate value for this variable will depend on the system and how extensive receptor ligand contacts are. A rough rule of thumb is to use four times the number of ligand heavy atoms. A value of 0 indicates that no orientation will be thrown out unless it has more than bump_maximum bad contacts (or does not meet the energy_maximum criterion).

energy_maximum

specifies the maximum Delphi electrostatic score (if scoring_option is 2) or force-field score (if scoring_option is 3 or 4) a ligand orientation can have and still be written out during a SINGLE mode run. Again, the purpose is to exclude the least interesting output; energy_maximum can be set very high (1.0e+6, for example) if one does not wish to constrain the results. The contact_minimum and energy_maximum constraints are applied independently. Only orientations meeting both constraints will be output if scoring_option is 2 or 3.

rmsd_override

is an override RMS deviation for SINGLE mode runs. All orientations having RMSD's(relative to the coordinates in the ligand input file ligand_atom_file, not including hydrogens) less than or equal to rmsd_override are written to output, regardless of score (of any type). If the user does not wish to increase the output over that subject to the constraints of contact_minimum and energy_maximum, but wishes to have RMSD's calculated, a value of 0.0 should be used. A negative value indicates that RMSD calculations will not be done. RMSD's are useful for comparing docked orientations to a crystallographically observed orientation.