rDock is a fast & free docking program designed to be used in High-Throughput Virtual Screening. This is a summary of the steps necessary to do so.

1) You mst have previously defined yor system & cavity (consult the manual)

2) Execute 50 docking runs for a set of ligands representative og your entire collection:

rbdock -i $f -o ${f}_out -r REC.prm -p dock.prm -n 50 > ${f}_out}.log

So, your output files are named *_out.sd. Create a report file:

sdreport -t *.sd > results_table.txt

Now execute 'ht_protocol_finder.pl' to identify the optimal threshold for HT-VS. If you execute the program without arguments, help is printed. The basic idea is that there is no need to perform exhaustive docking for every single molecule. We can start with a small number of runs (Genetic Algorithm optimizations). If the molecule reaches a reasonable docking score it will be worth continuing until completeness (50 docking runs). Otherwise, the molecule is unlikely to attain a good score and can be rejected earlier. 
This is how you execute it. To obtain a first guess of the values, you may take a look at the results table.

ht_protocol_finder.pl results_table.txt protocol.out -12 -15 5 15

After several trials, on of the predictions is:

 7.103, 21.880,  3.624,    5,  -15,   15,  -20 ***

This means that this 2-step process should be fairly efficient:

• Will need 7.1% of the time needed to perfomr exhaustive docking
• Will do 5 runs, and will continue if score reaches -15 (this will occur in 21.88% of cases)
• Then complete 15 runs and will continue if a score fo -20 is reached (will happen in 3.6% of cases)

If you are satisfied with these conditions, you have to create a 'filter file' with this information. 

3)