p. 7

In item (5), the instruction to use "make test.parallel" will not work, as there is no such target in the Makefile. Instead, use "make test.sander", "make test.sander.LES" and/or "make test.pmemd" to test the individual parallel programs.

p. 18

An additional set of tests of the ff03 force field has appeared: M.C. Lee and Y. Duan, Distinguish protein decoys by using a scoring function based on a new Amber force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins 55, 620-634 (2004).

p. 26

The "man9" example uses the "EP" version of the glycam04 force field, and has some minor glitches. Here is an improved version, prepared by Karl Kirschner, using the non-extra-point force field.

p. 28

There is an additional unit, T4E, and corresponding box, TIP4PEWBOX, that provide an "Ewald" version of the TIP4P water model. See H.W. Horn, et al., Development of an improved four-site water model for biomolecular simulations: TIP4P-EW. J. Chem. Phys. 120, 9665-9678 (2004).

p. 48

In Amber8, the leaprc files assign residue HIS to HIE, not to HID. This can be overridden either by assigning the protonation states directly in your pdb files, or by modifying the leaprc files.

p. 53

Bugfix.42 changes the format of the bond command. Bond orders are now specified by S, D, T, A for single, double, triple or aromatic bonds respectively. This replaces the old specification which used -, =, # or :.

p. 61

The PREP input file example for LEaP's loadAmberPrep command is missing a line: it should contain a blank line for record two, the NAMDBF record. See the PREP File Format.

p. 69

There is an additional option for the set default command: set default gibbs [on|off]; this option is described on p. 34.

p. 83

The third line in the leap.in file (box in the middle of the page) should read "TP = loadMol2 tp.mol2". Without the "TP =" part, LEaP will not assign the correct name to the unit.

p. 96

Don't set ntx to 7 if you have a non-periodic system; better yet, don't set ntx to 7 under any circumstances.

p. 109

The use_pme variable is no longer a legal input parameter; it is set automatically based on other input options.

p. 141

In Section 5.17, only the variables ifqt, nqt, idc and labels are actually implemented.

p. 151

The method for constant pH simulations has been published: J. Mongan, D.A. Case and J.A. McCammon. Constant pH molecular dynamics in generalized Born implicit solvent. J. Comput. Chem. 25, 2038-2048 (2004).

p. 208

For the analyze timecorr command, the "vec2 vecname2" argument pair is required, and not optional. If autocorrelation functions are needed, "vecname2" can be the same as "vecname1". (2004).

p. 241

For protonate, the -b, -c, -al, -ae and -ap options are not implemented (or needed). There is an additional -r option to renumber residues starting at 1.

p. 252

The pbsa program automatically performs two FDPB calculations, with an electrostatic focusing method. The first FDPB grid extent is set by an additional variable, FILLRATIO: the grid is FILLRATIO times the solute size (in each of the x, y and z directions); default is 2.0. The grid spacing of this first calculation is 8 times as large as that specified by the SPACE variable. The electrostatic potential from the first calculation is then used to set the boundary condition for the second FDPB calculation. The second FDPB grid extent is set to be just large enough to enclose the solute with a buffer zone between the solute surface and the grid boundary. The buffer zone is thick enough to cover the solvent probe. The grid spacing is that specified by SPACE. If the first FDPB grid is smaller than the second FDPB grid, the program will issue a warning and exit. Hence, for very small solutes, it may be necessary to set FILLRATIO to a larger value (such as 4) in order to complete the calculation.

In this implementation, the reaction field energy is output in both the EEL and ERF fields; hence, unlike sander, the EEL field does not contain the Coulomb energy, but just a piece of it.

p. 286

Line 6 should read: TEQ : the equilibrium angle for the angles of each type, radians

p. 295

Reference [4] has now been published: J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman and D.A. Case. Development and testing of a general Amber force field. J. Comput. Chem. 25, 1157-1174 (2004). Please note that in Eq. (5) of this paper, the bond angle theta(ijk) should be raised to the power -1/2, not -2; [see J. Comput. Chem. 26, 114 (2005).]

Reference [8] has also been published: A. Onufriev, D. Bashford and D.A. Case. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 55, 383-394 (2004).