SDA example run "bnbs"

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

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

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Barnase and barstar association example

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

2 types of simulations are done in this example: simulations without the non-polar desolvation term (similar to ones done with SDA version 4) and simulations with a weak non-polar desolvation term (with the proportionality factor of -13 cal/mole per 1 Ų buried surface area).
The results are summarised in the figures below.

Simulations with only electrostatic terms reproduce the experimental association rate when the formation of 2 contacts at ~6Å is used as the criterion for formation of an encounter complex.  Simulations with the weak non-polar term included result in formation of encounter complexes at a ca. 10 times higher rate at a range of contact distances and number of contacts. Namely, 3 or 4 contacts are formed at the same rate with contact distances from 4 to 10 Å.  At contact distances of ~ 4 Å, formation of 2 or 3 or 4 contacts occurs at the same rate.


Residence times are calculated afterwards using sda-koff.  A typical result looks like this:

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December 2007; October 2010