3. Iterative Optimizations
This simulation became accurate by the peptide collision with water molecules, residues received larger torques, and planar amino acids to rotate faster. The length of the side chain was estimated as the maximum of bonds from the Cα atom. The order of calculation of the pair of bonds of the residue from the sum of the priority from torsional property.
The 8 amino acids of 1n9v were arranged into ‘D(7)R(2)V(8)Y(1)I(5)H(4)P(6)F(3)’. The smaller number was calculated first and received higher priority.
Consequently, the 4th peptide bond between Tyr(Y) and Ile(I) was first calculated(1+5=6), and the bond between Tyr(Y) and Val(V)(1+8=9). The order of priority is ‘D-(3)-R-(4)-V-(2)-Y-(1)-I-(6)-H-(7)-P-(5)-F’. The numbers in the round brackets designate the order of the linkage among residues. The dihedral angles flanking peptide bond are φ and ψ angles. Between these two dihedral angles, we calculated the one close to the higher priority first, and the other close to the lower priority later.
In this order, we iteratively optimized the initial structure from cotranslational folding. This was performed until the convergence of potential energy. The structure in which potential energy converged in six times from the initial structure was taken.