Parameter Table

keyword	variable name	allowed values	default
ratio_minimum	ratiom	0.0 - 1.0	0.0
atom_minimum	natmin	integer	1
atom_maximum	natmax	integer	80
restart	restr	yes no	no
number_save	nsav	integer	100
normalize_save	nnsav	integer	0
molecules_maximum	moltot	integer	10000
restart_interval	molsav	integer	100
initial_skip	molskp	integer	0

Parameter Descriptions

ratio_minimum

gives the minimum value of the ratio of the longest ligand internal distance to the longest receptor internal distance. The purpose of this variable is to filter out molecules that are not capable of filling the site very well. Ligands whose longest internal distances are too short according to this criterion are skipped. Allowed values range from 0.0 to 1.0; any value outside this range is set to 0.0. A value of 0.0 means that no ligands are removed from consideration based on their longest internal distances. A value of 1.0 means that a ligand must be capable of at least spanning the two farthest-apart spheres in the cluster being used for docking.

atom_minimum

specifies the minimum number of heavy (nonhydrogen) atoms a molecule must have in order to be examined during a SEARCH run. Molecules having fewer heavy atoms are skipped. Values less than or equal to 0 default to 1.

atom_maximum

specifies the maximum number of heavy (nonhydrogen) atoms a molecule can have and still be examined during a SEARCH run. Molecules having more heavy atoms are skipped. Values less than or equal to 0 default to 80.

restart specifies whether or not the SEARCH run will be a restart. During a restart run, information is read from the ligand output files specified in output_file_prefix. The restart feature is useful because runs can pick up where they were stopped by a system crash, or by being killed. The information stored for restarts includes: the number of molecules examined so far, the number the user wishes to save for each type of score, pointers to the molecules that have the top scores so far, and the corresponding rotation/translation matrices. Do not be alarmed to see non-PDB-format output during a run or after a run is terminated abnormally; it is merely the restart information. In the present implementation, the profile listed in OUTDOCK describing the number of ligands in a particular contact score range only includes the molecules examined in the current run. The minimum, mean, and maximum contact scores are for the entire database (both pre- and post-restart), as is the total number of molecules examined. Before restarting, one should give the original OUTDOCK a different file name, as the program will try to create another OUTDOCK.

number_save

specifies the number of ligands that will be saved for each kind of score, during a SEARCH run. The number_save top-scoring molecules will be written out in their best-scoring orientations. Values less than 0 default to 100.

normalize_save

specifies the number of ligands that will be saved for each type of score, after normalization by dividing by the number of heavy atoms, during a SEARCH run. The normalize_save top-scoring (after normalization) molecules will be written out in their best-scoring orientations. The output file name is derived from output_file_prefix by appending the string norm. If normalize_save is not specified or is set to a negative number, it defaults to 0.

molecules_maximum

specifies the total number of molecules to be examined in the SEARCH run. If the database has fewer than molecules_maximum molecules, all of the molecules will be examined (except for those skipped at the beginning of the database, if any - see initial_skip below). If the database has more than molecules_maximum molecules, then PDB output will be generated after molecules_maximum molecules have been examined.

restart_interval

indicates how often restart information will be saved during a SEARCH run. Restart information will be saved every restart_interval molecules. An exception is when restart_interval molecules. An exception is when molecules_maximum molecules have been examined, in which case the final PDB output is generated.

initial_skip

specifies the number of molecules at the beginning of the database that will be skipped. If initial_skip is not specified, it is set to 0.