Amber 9 Users' Manual Additions and Corrections

p. 17 The 4 lines beginning: water.in, meoh.in, chcl3.in and nma.in should consist of a single line which reads:
solvents.lib library for water, methanol, chloroform, NMA, urea.

p. 22 Consult the original reference (not Chap. 12.2) to see the charge-fitting method for the Cornell et al. force field.

pp. 87,90 The "-y" flag to sander does not work as documented. Use "-x" instead of "-y" when setting imin=5.

p. 92 When ioutfm is set to 1 (for binary trajectories), the coordinates written to the netCDF files are never "wrapped", no matter what the value of iwrap. Basically, this means you should always use iwrap=0 when ioutfm=1. This limitation applies to both sander and pmemd.

p. 94 For Langevin dynamics, the position of the center-of-mass of the molecule is reset to zero every NSCM steps, but the velocities are not affected. Hence, there is no change to either the translation or rotational components of the momenta. (Doing anything else would destroy the way in which temperature is regulated in a Langevin dynamics system.) The only reason to even reset the coordinates is to prevent the molecule from diffusing so far away from the origin that its coordinates overflow the format used in restart and trajectory files.

p. 121 The default value of RDT is 0.0, not 0.01.

p. 154 The only accepted value for the multiplicity (spin) of the QM system is 1.

p. 154 In the explanations of variables at the top of the page, references to Eqs. (4), (5), (6) and (8) should be to (6.21), (6.22), (6.23) and (6.25), respectively.

p. 157 At the bottom of the page, the explanations for TGTRMSMASK and TGTFITMASK are reversed. The description in the first paragraph of Section 6.6 is correct.

p. 158 There is a new web site for Alan Grossfield's WHAM program: http://membrane.urmc.rochester.edu/.

p. 236 The paper referred to in line 5 is C. Simmerling and R. Elber. Hydrophobic "collapse" in a cyclic hexapeptide: Computer simulations of CHDLFC and CAAAAC in water. J. Am. Chem. Soc. 116, 2534-2547 (1994).

p. 299 Appendix C indiates that dsum_tol and ew_coeff have been "retired". This is incorrect: these variables are still present, with their original meanings.

p. 302 Reference [6] has now been published: L. Yang, C. Tan, M.-J. Hsieh, J. Wang, Y. Duan, P. Cieplak, J. Caldwell, P.A. Kollman, R. Luo. New-generation Amber united-atom force field. J. Phys. Chem. B 110, 13166-13176 (2006).

p. 302 Reference [11] has now been published: J. Mongan, C. Simmerling, J.A. McCammon, D.A. Case, and A. Onufriev. Generalized Born model with a simple, robust molecular volume correction. J. Chem. Theory Comput. 3, 156-169 (2007).

p. 303 Reference [26] has now been published: V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725 (2006).

p. 303 Reference [30] has now been published: Z.-X. Wang, W. Zhang, C. Wu, H. Lei, P. Cieplak, and Y. Duan. Strike a Balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J. Comput. Chem. 27, 781-790 (2006). Erratum: ibid., 27, 994 (2006).

p. 303 Reference [33] has now been published: A.M. Wollacott and K.M. Merz, Jr. Development of a parameterized force field to reproduce semiempirical geometries J. Chem. Theory Comput. 2, 1070-1077 (2006).

p. 305 Reference [56] is somewhat mangled; the correct citation is: J. Wang, W. Wang, P.A. Kollman, and D.A. Case. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Model., 25, 247-260 (2006).

p. 307 Reference [101] has now been published: G. Sigalov, A. Fenley, and A. Onufriev. Analytical electrostatics for biomolecules: Beyond the generalized Born approximation. J. Chem. Phys. 124, 124902 (2006).

p. 309 Reference [131] has now been published: R.C. Walker, M.F. Crowley, and D.A. Case. The implementation of a fast and efficient hybrid QM-MM potential method within The Amber 9.0 sander module. J. Computat. Chem. 29, p. 1019 (2008).

p. 313 The author list in Ref. [206] is incorrect. The citation should read: J. Srinivasan, T.E. Cheatham, III, P. Cieplak, P.A. Kollman and D.A. Case. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120, 9401-9409 (1998).

p. 17	The 4 lines beginning: water.in, meoh.in, chcl3.in and nma.in should consist of a single line which reads: solvents.lib library for water, methanol, chloroform, NMA, urea.
p. 22	Consult the original reference (not Chap. 12.2) to see the charge-fitting method for the Cornell et al. force field.
pp. 87,90	The "-y" flag to sander does not work as documented. Use "-x" instead of "-y" when setting imin=5.
p. 92	When ioutfm is set to 1 (for binary trajectories), the coordinates written to the netCDF files are never "wrapped", no matter what the value of iwrap. Basically, this means you should always use iwrap=0 when ioutfm=1. This limitation applies to both sander and pmemd.
p. 94	For Langevin dynamics, the position of the center-of-mass of the molecule is reset to zero every NSCM steps, but the velocities are not affected. Hence, there is no change to either the translation or rotational components of the momenta. (Doing anything else would destroy the way in which temperature is regulated in a Langevin dynamics system.) The only reason to even reset the coordinates is to prevent the molecule from diffusing so far away from the origin that its coordinates overflow the format used in restart and trajectory files.
p. 121	The default value of RDT is 0.0, not 0.01.
p. 154	The only accepted value for the multiplicity (spin) of the QM system is 1.
p. 154	In the explanations of variables at the top of the page, references to Eqs. (4), (5), (6) and (8) should be to (6.21), (6.22), (6.23) and (6.25), respectively.
p. 157	At the bottom of the page, the explanations for TGTRMSMASK and TGTFITMASK are reversed. The description in the first paragraph of Section 6.6 is correct.
p. 158	There is a new web site for Alan Grossfield's WHAM program: http://membrane.urmc.rochester.edu/.
p. 236	The paper referred to in line 5 is C. Simmerling and R. Elber. Hydrophobic "collapse" in a cyclic hexapeptide: Computer simulations of CHDLFC and CAAAAC in water. J. Am. Chem. Soc. 116, 2534-2547 (1994).
p. 299	Appendix C indiates that dsum_tol and ew_coeff have been "retired". This is incorrect: these variables are still present, with their original meanings.
p. 302	Reference [6] has now been published: L. Yang, C. Tan, M.-J. Hsieh, J. Wang, Y. Duan, P. Cieplak, J. Caldwell, P.A. Kollman, R. Luo. New-generation Amber united-atom force field. J. Phys. Chem. B 110, 13166-13176 (2006).
p. 302	Reference [11] has now been published: J. Mongan, C. Simmerling, J.A. McCammon, D.A. Case, and A. Onufriev. Generalized Born model with a simple, robust molecular volume correction. J. Chem. Theory Comput. 3, 156-169 (2007).
p. 303	Reference [26] has now been published: V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725 (2006).
p. 303	Reference [30] has now been published: Z.-X. Wang, W. Zhang, C. Wu, H. Lei, P. Cieplak, and Y. Duan. Strike a Balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J. Comput. Chem. 27, 781-790 (2006). Erratum: ibid., 27, 994 (2006).
p. 303	Reference [33] has now been published: A.M. Wollacott and K.M. Merz, Jr. Development of a parameterized force field to reproduce semiempirical geometries J. Chem. Theory Comput. 2, 1070-1077 (2006).
p. 305	Reference [56] is somewhat mangled; the correct citation is: J. Wang, W. Wang, P.A. Kollman, and D.A. Case. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Model., 25, 247-260 (2006).
p. 307	Reference [101] has now been published: G. Sigalov, A. Fenley, and A. Onufriev. Analytical electrostatics for biomolecules: Beyond the generalized Born approximation. J. Chem. Phys. 124, 124902 (2006).
p. 309	Reference [131] has now been published: R.C. Walker, M.F. Crowley, and D.A. Case. The implementation of a fast and efficient hybrid QM-MM potential method within The Amber 9.0 sander module. J. Computat. Chem. 29, p. 1019 (2008).
p. 313	The author list in Ref. [206] is incorrect. The citation should read: J. Srinivasan, T.E. Cheatham, III, P. Cieplak, P.A. Kollman and D.A. Case. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120, 9401-9409 (1998).