Molecular Modeling and Simulation: An Interdisciplinary Guide

Tamar Schlick

Text Corrections and Addenda

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 low-resolution 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:           S. Lifson and A. Warshel, 1968. Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n-Alkane Molecules, J. Chem. Phys. 49: 5116-5129.           M. Levitt and S. Lifson, 1969. Refinement of Protein Conformations using a Macromolecular Energy Minimization Procedure, J. Mol. Bio. 46: 269-279.           M. Levitt, 2001. The Birth of Computational Structural Biology, Nature Struc. Biol. 8: 392-393.
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, Computer Simulation of Chemical Reactions in Enzymes and Solutions. John Wiley & Sons (Printed in the United States), 1991.           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: 227-249.           A. Warshel and S. T. Russell, 1984. Calculations of Electrostatic Interactions in Biological Systems and in Solutions, Q. Rev. Biophys. 17: 283-422.
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'-to-3' vector going upward. The new figure is attached Figure 5.1.