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.
cd bnbs_energy/
../../../bin/sda_flex sda_energy.in > out_sda_energy
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.
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:
- Non-polar interactions (always negative) compensate favorably the electrostatic desolvation terms (always unfavorable).
Note: This is the case in this specific example, this is not always so! - The energy of the first representative, -16.5 kT, is much higher (less negative) than in the simulation in which all interactions are present (-22.5 kT).
sda_energy provides the possibility to test hypotheses on the nature of the favorable or unfavorable energy terms, but the terms must be present during the Browninan Dynamics simulations to produce complete quantitative results