# Internal Energy Calculation

During growth and minimization, an internal energy scoring function can be used. The goal of the internal energy function is to reduce the occurrence of internal clashes during the torsional optimization. This function computes the repulsive Lennard-Jones term between all ligand atom pairs, excluding all 1-2, 1-3, and 1-4 pairs. (Currently, attractive Lennard-Jones and Coulombic terms are neglected; he aim is to eliminate internal clashes not to optimize the internal geometry. in addition, since there is no dihedral term in the force field, if the attractive terms are included the molecule might appear less physical.) The internal energy can be cut on or off; if cut on, it is all ways used and is reported in the final energy. If it is cut of it is never used. The pruning during growth is done by considering both the internal and interaction energies. We recommend the use of the internal energy function for all calculations.

# Internal Energy Parameters

use_internal_energy [yes] (yes no): #Flag to use Internal energy (only repulsive VDW) for growth and/or minimization internal_energy_rep_exp [12] (int): #The VDW exponent