MacroModel Reference Manual - ISP

Chapter 4: Operation Codesway on the arrangement of large number of atoms in the system. The ASET mechanism takes astatic approach to calculating the GB solvation energy in which this dependence of the Bornradii is ignored, leaving a simple pairwise sum of solvation terms. The surface area (SA)portion of the solvation energy calculation is more problematic because from a single conformationit is not obvious how much the surface area is affected by association. Also, because thesolvent inaccessible regions are often excluded by multiple atoms, a pairwise breakdown of theenergy solvation energy is problematic. The ASET mechanism takes a simple approach in thatit associates the SA solvation term with the interaction of a set with itself.ASET commands may be issued before a READ, and are in force for all subsequent structuresread until or unless cleared or altered. Thus, such commands may be issued before a BGIN/END loop, and will be in force for all structures read within the loop.Arg7 and arg8 are only used when MBAE is not used.arg1-4arg5arg6Atom numberThe action that is applied to these atoms depends on the settings of arg5 and arg6. Ifarg1-4 are all zero, then the action is applied to all atoms in the system.Set numberMay be any non-negative integer, specified as 0.0000, 1.0000, 2.0000, etc. Only setsone through 20 will be considered during a subsequent ELST. Set 0 stands for noset; placing an atom in Set 0 is the equivalent of removing it from whatever set ithad been in. Recall that the sets are non-overlapping: an atom is a member of onlythe last set into which it is placed.Command modeShould be given