We have calculated the electrostatic potentials and charges for our proteins, so we have everything we need to calculate forces. During the course of the simulation however, we need to be able to determine when we have formed a bound complex. In this case, this is relatively easy since we have a bound structure of barnase and barstar we can use.
To set up the reaction sites on each protein, we use a program called da-pairs that finds donor and acceptor pairs (hydrogen bonds) between the two proteins. It looks for input files named 1.pdb and 2.pdb, so we can create links to these filenames using our pqr files
ln -s barnase.pdb 1.pdb
ln -s barstar.pdb 2.pdb
Now when you run da-pairs, it will create new files called 1_rxna and 2_rxna which are the reaction site atoms on proteins 1 and 2 respectively. There was also a file called da.distance created. If you look at that file, it states that the default distance used for finding donor-acceptor pairs was 6.0 A. That is too large, so edit this file changing the 6 A to 4 A and re-run da-pairs. Once that finishes, you can rename your rxna files for the appropriate protein
mv 1_rxna barnase.rxn
mv 2_rxna barstar.rxn
We have the reaction sites set up, now we are ready to set up the actual BD simulation.