q1:
Load the trajectory file in VMD ( the files you need are in a compressed folder on blackboard).
Calculate the RMSD, contact map along the trajectory time. Explain what the RMSD, contact map are, and what information they provide. (10 points)
Calculate the distance between residue 56 atom O and residue 290 atom CA. (5 points)
Calculate the Phi and Psi angles of residue 299 along the trajectory time. (10 points)
q2: Go to the PDB databank and download the structure of 2HHB.
Sample Solution
