The notebook MDRestraintsGenerator.ipynb uses MDRestraintsGenerator to scan the backbone atoms of a given coiled coil complex or intermediate state and outputs the most stable residues, which can form the basis of anchor points for Boresch restraints. Requires: 1) topology .prmtop file of coiled coil complex or intermediate state, 2) trajectory .dcd file of unbiased MD simulation in the case of a full coiled coil complex, or MD simulation with RMSD restraints on the backbone in the case of intermediate states restricted to their "open" conformations, 3) residue indices of the "ligand" and "receptor" helices.
The notebook Boresch_Restraints_Distributions.ipynb calculates the distributions of the Boresch angles and dihedrals for pre-selected anchor points on Cα atoms. Requires: 1) topology .prmtop file of coiled coil complex or intermediate state, 2) trajectory .dcd file of unbiased MD simulation in the case of a full coiled coil complex, or MD simulation with RMSD restraints on the backbone in the case of intermediate states restricted to their "open" conformations, 3) PDB file generated during parameterisation with tleap (pdb_from_tleap.pdb).
The file restraint_anchor_points.csv contains the anchor points used for the Boresch restraints for each complex and intermediate state, and the equilibrium values of the Boresch angles and dihedrals. Each anchor point is the Cα atom of the respective residue. Angles and dihedrals are reported in degrees.