Structural-dynamical model restricted rotators

The positions of the C and Cp atoms from the CG model are used to position the N and C backbone atoms so that the correct chirality is maintained (o-amino acids). To restrict the rotational freedom, a strong constraint was used, namely that neighbouring residues must have a planar peptide bond. Harmonic potentials were added between neighbouring backbone atoms, the equilibrium distances of which were taken from average distances calculated from the PDB structures. The C atoms were then immobilised by setting their masses to infinity, and a short molecular dynamics simulation was then run to relax the system. 

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