The following changes are required to the first printing of the Amber 4.0 manual. (Later printings are numbered on the second page.) ************************Minmd section, page 81, item 11.4 ************Original 11.4 DIELC Dielectric multiplicative constant for the electrostatic interactions. If DIELC .le. 0.0 then DIELC = 1.0. DIELC and IDIEL are coupled. For example to obtain a dielectric constant of 4rij set DIELC=4 and IDIEL=1. ************Should read 11.4 DIELC Dielectric multiplicative constant for the electrostatic interactions. If DIELC .le. 0.0 then DIELC = 1.0. DIELC and IDIEL are coupled. For example to obtain a dielectric constant of 4rij set DIELC=4 and IDIEL=0. ^ | ************************Gibbs section, page 105, paragraph 1 Original GIBBS 4.0 is built upon the original (3.0) version of this code, which was written by U.C. Singh and P.A. Kollman (UCSF), using numerous MD routines adapted from GROMOS83 by W.F. van Gunsteren. Should read (additional credit) GIBBS 4.0 is built upon the original (3.0) version of this code, which was written by U.C. Singh and P.A. Kollman (UCSF), using numerous MD routines adapted from GROMOS83 by W.F. van Gunsteren. Speedups to non-bonded pairlist generation and residue-based imaging adopted from code written by George Seibel for AMBER revision 3A. ************************Gibbs section, page 120 ************Original 10.2 NTID Read, but not used. ************Should read 10.2 NTID Flag for solvent pairlist behavior. = 0 only the first atom of each solvent molecule is used when generating the non-bonded pairlist for a periodic system (for water, this is the oxygen). If this atom lies within the specified cutoff, the entire solvent molecule is included in the non-bonded pairlist. This can result in a substantial speedup in non-bonded pairlist generation, and is recommended when using water as the solvent. =86 all atoms in a solvent molecule are considered when generating the non-bonded pairlist for a periodic system. If any atom of the solvent molecule lies within the specified cutoff, all atoms of the solvent molecule will be included in the non-bonded list. This is the behavior of versions of AMBER <= 3.0. A value of NTID=0 is suggested for calculations using water as a solvent. For calculations using larger solvent molecules, one should carefully consider whether using only the first atom is appropriate. NTID will have no affect for non-periodic systems. ************************Gibbs section, page 130 **********Original 14a.3 ISLP Determines the direction in which the slope is calculated. = 1 the slope is calculated in the forward (0->1) direction =-1 the slope is calculated in the reverse (1->0) direction = 2 the slope is calculated using the average of the forward and reverse energies. For best results, the slope should be calculated in the same direction as the simulation, or as the average of the forward and reverse energies. The default behavior (ISLP=0) is to calculate the slope in the same direction as the simulation. With thermodynamic integration, or when double-wide sampling is defeated, ISLP has no effect. **********Should read 14a.3 ISLP Determines the direction in which the slope is calculated. = 0 (default) use the appropriate value of ISLP (-1 or 1) to calculate the slope from energies calculated in the same direction as the simulation (recommended). = 1 the slope is calculated from the forward (0->1) energy at each step. =-1 the slope is calculated from the reverse (1->0) energy at each step. = 2 the slope is calculated using the average of the redundant free energy values (from double wide sampling) over the interval in the direction opposite to the simulation, i.e. G(reverse[curr window] - G(forware[prev window])/2 or G(forward[curr window] - G(reverse[prev window])/2 for simulations run 0->1 and 1->0, respectively. This option can be useful when very few points are used to evaluate each slope (e.g. IAVSLP = 2). = 3 the slope is calculated using the average of the forward and reverse energies at each lambda. For best results in most cases, the slope should be calculated in the same direction as the simulation. This is the default behavior (ISLP=0). With thermodynamic integration, or when double-wide sampling is defeated, ISLP has no effect. Only options ISLP=0 or ISLP=3 should typically be used when AMXRST > 0.