MacroModel Reference Manual - ISP

Chapter 4: Operation CodesCOPY — COPY coordinatesCopies the current set of coordinates to a reference array for later use. The reference array iscurrently only used by the ALGN command.ALGN — ALiGN with reference coordinatesAligns the current system’s coordinates with the reference system coordinates. Alignment canbe conducted by center of mass or principal axis or both. The reference coordinates must havealready been saved using COPY. ALGN may be used in a BGIN/END loop and is intended to prepositionmolecules prior to further processing with commands like MINI and MBAE. Tosavealigned structures in the output structure an explicit WRIT statement is needed unless arg3 is 5(see below).If you use ALGN with MBAE and want to specify substructures with SUBS, you must set arg2 ofSUBS to 1 to ensure that the correct substructures are used.arg1Type of alignment0,1 Reposition the current system so that its center corresponds to that in the referencesystem.2 Reorient the current system so that the principal axes of the current system correspondto those in the reference system.3 Reposition and reorient the current system so that its center and principal axes correspondto those in the reference system.arg2Atom weighting0, 1 Mass-weight the coordinates when calculating the system center and principal axis.2 Weight all atoms equally when calculating the system center and principal axes.arg3Principal axis alignmentThis argument is only used if arg1 is 2 or 3.0, 1 Closest principal axis alignment.2 Rotate by 180 degrees about the first principal axis relative to the closest principalaxis alignment.3 Rotate by 180 degrees about the second principal axis relative to the closest principalaxis alignment.82MacroModel 9.7 Reference Manual