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Barnase-barstar interaction energy

This example shows how to compute the interaction energies of a set of configurations of two solutes. It requires all pdb structures and grids precomputed in data_grid/ as input. You need to run the script in prepare_grid_and_ecm/ at least once to generate the grids and effective charges in this folder.

Running the example

cd bnbs_energy/
../../../bin/sda_flex sda_energy.in > out_sda_energy
Details of the script

The script will run a sda_energy computation. It recomputes the energy from a set of configurations read from a complexes file.

In this example case, we used the representative clusters generated in bnbs_docking/ with the simulation containing only the electrostatic energy terms. This restart file, complexes_only_elect_clusters, has been generated (manually) in bnbs_docking_hits/cluster_only_elect_c2c/.

The energy calculation allows the influence of the other energy terms (e.g. electrostatic desolvation and non-polar terms) on a set of predefined configurations, generated from a previous simulation or otherwise, to be checked quickly.

Description of the results

The output is a new trajectory file (keeping the order of the complexes) which contains the recomputed energies of interactions

In comparing the energies with the run in bnbs_docking_hits/, we see that the interactions are generally more favorable with all terms: