hen egg white lysozyme) in the second text window and click search. Usually you don t know the ID, so give the protein name (e.g. If you already know the PDB ID (1iee) you can type it in the first text window. Let s say that you are looking for hen egg white lysozyme (HEWL). a) Download the correct structure Go to PDB ( and look for protein structure you are interested in (Fig.2). Usually we are interested in large proteins and that is why calculations using the X-ray structure as a first example are described. The main difference between NMR and X-ray structures is that in NMR structures hydrogen atoms are included while there are no hydrogen atoms in X-ray structure (H atoms are too light to X-ray diffraction experiments). Due to technical reasons, X-ray structures are available for large proteins only. Such information is deposited in the PDB (protein data bank) which consist of X-ray as well as NMR protein structures. 3 To simulate the protein first we need the x,y,z coordinates of each atom in the protein.
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