The static partial structure flag. If you have partial structure to input, include this flag and follow it with the name of the PDB file containing the correctly positioned partial structure. You can separate the partial structure into as many files as you wish and use this flag multiple times on the command line. The minimum packing distance calculation will treat the partial structure within each separate file as a separate fragment. This will be MUCH slower, but if you have a very large search molecule and a workstation with little available memory, the FFT calculation may cause excessive swapping.
Summation uses little memory.
This only affects the single, initial FFT calculation and has no effect on the speed of the subsequent evolutionary search. This option is not necessary for normal operation of the program, but can be useful for testing purposes. If the seed is not set here, or is set to a value of zero, the seed is obtained from the system clock at run time. It will report the best score for each generation. At the end of the evolutionary search, a conjugate-gradient minimization is performed on the best scoring solution from the final generation.