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Protein: Proteins were selected to include a wide range of types. These cover: simple proteins, such as crambin and barnase; metalloproteins, e.g., myoglobin, and calmodulin; oligomeric proteins, e.g., hemoglobin and the potassium channel; and polymeric proteins such as silk and a collagen-like protein. The purpose of the tables of proteins is to show how to specify various types of proteins. The proteins are not intended to be used directly for modeling experiments. No checks have been done to ensure that the starting structures are chemically sensible. The suggested check - to verify that all charged sites are valid - has not been carried out.
ΔHf: Proteins from the PDB often lack hydrogen atoms. These have been added and their positions optimized, during this process, some salt bridges may form. The heat of formation represents the protein with the positions of the hydrogen atoms optimized. This is the starting geometry.
# Atoms: The number of atoms, heavy and light, in the protein. Where present, this includes atoms in small molecules and ions, such as water and sulfate.
Constrained 10 Average Motion: The starting geometry was allowed to relax, i.e., all geometric variables were optimized, but a restraint was imposed, that imposed a penalty of 10 kcal/mol for every Ångstrom2 an atom moved from its original position. The average motion is the average movement of each atom relative to the starting geometry.
Constrained 10 ΔHf: This is the heat of formation at the constrained energy minimum, i.e., at the geometry where the forces acting on the atoms are equal and opposite to those of the restraining function. The contribution of the restraining function are not included in this quantity.
Constrained 3 Average Motion: This is similar to the Constrained 10 average motion, but with the restraining function replaced with 3 kcal/mol/Å2.
Constrained 3 ΔHf: This is similar to the Constrained 10 ΔHf, but with the restraining function replaced with 3 kcal/mol/Å2.
Unconstrained Average Motion: The starting geometry was allowed to relax, i.e., all geometric variables were optimized, without constraint.
Unconstrained ΔHf: This is the heat of formation at the unconstrained energy minimum.