MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg1arg2arg5arg6IdentifierThis is an arbitrary integer that must have the same value as arg4 in some MINIcommand. In most typical use, both are zero.Number of iterations before preliminary energy testAfter this number of minimization iterations are done, a test will be performed tosee whether the current structure is less than the arg6 kJ/mol above the global minimumfound so far. A conservative value is 1/3-1/2 the number of iterations in theMINI command (arg3). Default: a very large number, implying that no preliminarytest will be performed.A reasonable value for arg2 is 1/3-1/2 of the number of iterations to give minimizationconvergence for a typical conformation, but it is wise to minimize severalconformations of the actual structure to see how many iterations are necessary tobring the energy to within several kJ/mol of its final value.Energy window for final testDefault: 0.0 (i.e., only the global minimum will be kept).Energy window for preliminary testA conservative value is twice arg5. Default: 0.0 (i.e., all minima will be kept).NORE — NO REordering done on output structuresNormally, MULT and conformational search output structures are reordered in increasingenergy. If this command is specified, this reordering is suppressed.NORE must come before READ or TRED commands.4.9 Coordinate ManipulationThe combination of the COPY and ALGN opcodes permits very rapid approximate alignment ofligands with a reference ligand using center of mass and moments of inertia. These commandsmay be used to crudely preposition ligands prior to an Embrace conformational search calculationbased upon the position of a reference ligand already positioned in the active site. Whilethis combination of commands may be useful the positioning is crude and the searching ofconformational space is slow and quite limited compared to that available in Schrödinger’sdocking program, Glide.Note that COPY/ALGN may require the purchase of a separate license.MacroModel 9.7 Reference Manual 81