SDA example run "bnbs-docking"

This example can be found in directory examples/bnbs-docking.
The following subdirectories are present in this directory:

run-hits/	Results of the example run script for barnase and barstar docking at HITS
data/	Data files (pdb and input files) needed for running the barnase and barstar docking example
doc/	Documentation
scr/	Scripts to do the example run

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Barnase and barstar docking example

The results of SDA runs can be found in the run-hits/ subdirectory or can be generated in a new run/ subdirectory using the script scr/bnbs-docking-prepare-and-run .  In order to execute this script locally, you need to define 2 parameters - the location of the SDA6 distribution directory and the location of the UHBD executable.
In addition, the location of the directory of the cluster program has to be set in data/run_clusterDPipe.sh

The script performs 3 simulations in which only the electrostatic interaction term is included (as in Motiejunas et al, 2008).
 These have a specific center-to-center distance reaction criterion and:
 1. the rotation of protein 1 is not taken into account (efast is set to True), 1000 trajectories are generated and 500 complexes are recorded for further analysis.
 2. The rotation of protein 1 is taken into account (efast is set to False), 250 trajectories are generated.
 3. At least 2 nonspecific  constraints (specified like reaction pairs in the association rate calculations, see the bnbs and bnbs-apbs examples)
 
 Then, clustering of the results of the first simulation is performed in the run-hits/ClusterDPipe/ .
 By default all 500 recorded complexes are used and 5 clusters are generated and their properties are listed in clust_DPipe.ou:

No.  ClSize ClFSize    Repr    ReprE     ClAE    CLAED  RepRMSD  CLFRMSD   ElDesE   HyDesE      LjE   CouElE   SuDesE     tElE
  1     147    9958     237   -7.011   -7.039    0.359    6.239   10.434    0.000    0.000    0.000   -7.011    0.000   -7.011
  2     142   10246     352   -6.770   -6.503    0.317   23.758   25.827    0.000    0.000    0.000   -6.770    0.000   -6.770
  3     115    7534      83   -7.618   -6.639    0.385   41.005   41.998    0.000    0.000    0.000   -7.618    0.000   -7.618
  4      58    3615     479   -6.580   -6.403    0.518   48.525   46.210    0.000    0.000    0.000   -6.580    0.000   -6.580
  5      38    2247      16   -8.744   -7.140    0.722   24.168   24.315    0.000    0.000    0.000   -8.744    0.000   -8.744