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28 Appendix XI: Script Commands
page 301/321
OPTIMIZER <initstring>
best found solution has not been improved for the last
iterationsgbterminate number of iterations. The best found solution found
is returned.
The default settings (using the MolDock search algorithm) from the Docking
Wizard will generate the following optimizer string:
OPTIMIZER cavity=false;popsize=50;scalingfactor=0.50;crossoverrate=0.90;
offspringstrategy=1;terminationscheme=0;earlytermination=0.01;
clusterthreshold=1.00;keepmaxposes=5
Another example using the MolDock SE search algorithm:
OPTIMIZER
populationsize=50;cavity=true;creationenergythreshold=100;posegenerator=10,10
,30;maxsimplex=750;simplexsteps=300;simplexdistancefactor=1
Notice: an easy way to generate a suitable initstring is to use the Docking
Wizard to generate and save a generated script.
NEW
Clears the current workspace:
All molecules are removed from the workspace.
molegro virtual docker – user manual