Computational Drug Discovery and Design

hEdi) of a precomputed step of equilibration (cMD). From these

estimations, we calculate the values ofEthrpandEthrdby adding a

quantity of energy per degree of freedom to the preestimated

average potentials in the form of multiples of alpha as described in

the following section.

From the 50 ns precomputed relaxation of the system we

obtained:

(a) Average total potential energyhEp(tot)i¼165576.6800 kcal/

mol.

(b) Average dihedral energyhEdi¼4508.4797 kcal/mol.

(c) Total number of atoms (Nbr Atoms)¼54,126 atoms.

(d) Number of protein residues (Nbr residues)¼351 residues.

Approximate energy contribution per degree of freedom:

(a) αP¼0.16 kcal/mol/atomNbr Atoms (seeNote 9)

¼0.16 * 54126¼8660.16 kcal/mol.

(b) Ethrp¼hEp(tot)i+ (0.16 kcal/mol/atomNbr Atoms)

¼165576.6800 + (0.1654,126)¼156916.52 kcal/

mol.

(c) αD¼0.2(4 kcal/mol/residuesNbr residues) (seeNote

9 )

¼0.2(4351)¼280.8 kcal/mol.

(d) Ethrd¼hEdi+ (4 kcal/mol/residuesNbr residues)

¼4508.4797 + (4351)¼5912.4797 kcal/mol.

Fig. 1Schematic representation of the biased potential, the threshold boost

energyEthrand the normal potential

412 Sonia Ziada et al.