Brief instructions on how to run rdock

You need to have the following in your .cshrc - or make a file called .rdock 
containing these three lines and source .rdock before you need to use it.

setenv RBT_ROOT /y/programs/rdock/release_FC3
setenv PATH ${PATH}:${RBT_ROOT}/bin
setenv LD_LIBRARY_PATH ${RBT_ROOT}/lib

This is for the example of 5abp.  Copy the files you need from

/y/programs/testdata/rod

1. The input protein needs to be in Tripos mol2 format with appropriate atom typing and charges applied

2. The input ligand needs to be in SD format.  Usually there is a file for a reference ligand as well (in testing this is the actual structure)

3. First, you need to generate a receptor cavity file.  

rbcavity -r5abp.prm -was

5abp.prm refers to the protein file (5abp.mol2) and a reference ligand - 5abp_c.sd

4. Then you can run the docking program as:

rbdock -r5abp.prm -i 5abp_l.sd -o 5abp_test -p dock.prm -n 10

where 5abp_l.sd is the input ligand, 5abp.prm the parameter file from before, dock.prm the docking protocol and n the number of runs to be performed.  5abp_test is the root name of the output files.

