AMBER 6 MANUAL UPDATES

• pp. 27,30,31: ntp=2 is no longer supported; please change this variable in all input files to ntp=1.

• p. 130: The command-line flag to sander given as -rad in the manual should be -radii.

• p. 135: The variables NTWXM, NTWVM and NTWEM are no longer present in sander; the effect is as if these variables were disabled.

• p. 136: The cut variable can be used to specify the nonbonded cutoff, in Angstroms. For PME, this is used to limit the direct space sum, and the default of 8.0 is usually a good value. When igb>0, the cutoff is used both to truncate nonbonded pairs (on an atom-by-atom basis) and to ignore distant pairs in computing the effective Born radii (when igb=1); here a value larger than the default is generally required.

• p. 137: The paragraph on memory usage when igb=1 is out of date: the extra memory required for GB runs is about 7N words.

• p. 137: When igb=1, the salt concentration (in Molar units) can be specified by the saltcon variable; default is 0.0, or no added salt.

• p. 138: After SCEE, add the NSNB variable. This is active only when igb=0 and when nbflag=0. See the descrption of NBFLAG for more information.

• p. 139: The ibelly=1 option is not available when igb=1; the belly must correspond to the first atoms in the system when igb>1.

• p. 141: The first sentence describing tautp should read: "Time constant for heat bath coupling for the system."

• p. 144: There is an exception to the rule that iscale should always be zero: when direct dipolar couplings are used (see the description on p. 172 of the manual), then iscale should be set to 5.

• p. 172: Iscale should be set to 5 whenever direct dipolar coupling restraints are used.

• p. 262: NTWXM is now the minimum time for which coordinate snapshots will be dumped, i.e. there will be no snapshots recorded for the first NTWXM steps; after that, coordinates will be dumped every NTWX steps. Similarly for NTWVM and NTWEM. The intent is that snapshots might not be needed for an initial equilibration period.