1 
On p. 282, equation (9.43) should have in the denominator
instead of
.
(This typo has been corrected in the Fall 2004 reprinting of the book.) 


2 
On page 9, in describing the history of molecular mechanics and dynamics, important works must be added, after line 2, as follows: 
In 1969, following the pioneering Cartesian coordinate treatment described
by Lifson and Warshel a year earlier [Lifson and Warshel, 1968], Levitt
and Lifson reported the first energy calculation on entire protein
molecules (myoglobin and lysozyme), in which molecular potentials and
experimental constraints defined the target energy function minimized in
Cartesian coordinates by the steepest descent method to refine
lowresolution experimental coordinates [Levitt and Lifson, 1969]. Such
formulations in Cartesian coordinates paved the way for all subsequent
energy minimization and molecular dynamics calculations of biomolecules.
In fact, Warshel's recognition in the mid 1960s that programming molecular
force fields in Cartesian coordinates rather than internal coordinates
[Lifson and Warshel, 1968] led to efficient evaluation of the functions
along with analytic first and second derivatives and to program segments
in many current macromolecular modeling programs [Levitt, 2001]. References:
M. Levitt and S. Lifson, 1969. Refinement of Protein Conformations using a Macromolecular Energy Minimization Procedure, J. Mol. Bio. 46: 269279. M. Levitt, 2001. The Birth of Computational Structural Biology, Nature Struc. Biol. 8: 392393. 

3 
On page 509, item added to the reference list of Appendix C is: 
34. A. Warshel, Computer Simulation of Chemical Reactions in Enzymes
and Solutions. John Wiley & Sons (Printed in the United States), 1991. [Excellent reference text in the field of computational biological chemistry, particularly studies of enzymatic reactions. From basic principles of chemical bonding and enzyme mechanisms, the authors describe the governing force fields for molecular simulations, associated algorithms, various approaches to modeling chemical reactions, and examples of different mechanisms.] 

4 
On page 9, the following sentence is added at end of penultimate paragraph: 
Important concepts in protein electrostatics and enzyme/substrate
complexes in solution laid by Warshel and colleagues [Warshel and
Levitt, 1976; Warshel and Russel, 1984] paved the way to quantitative
modeling of enzymatic reactions and hybrid quantum/molecular mechanics
methods [Warshel, 2001]. References:
A. Warshel and M. Levitt, 1976. Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of Carbonium Ion in the Reaction of Lysozyme, J. Mol. Biol. 103: 227249. A. Warshel and S. T. Russell, 1984. Calculations of Electrostatic Interactions in Biological Systems and in Solutions, Q. Rev. Biophys. 17: 283422. 

5 
On page 391, the correct title of subsection 12.2.5 should be: "Hybrid Quantum/Classical Mechanics Methods". 
6 
On page 70, proline should appear with an NH2^{+} or NH instead of NH3^{+}. 
7 
On page 120, Figure 5.1, figure labels should be corrected as follows: 
The 3' and 5'ends have to be reversed, and strands I and II should be exchanged. According to the Cambridge Convention, when looking into the minor groove, STRAND I is on your left, with the 5'to3' vector going upward.
The new figure is attached
Figure 5.1.  