MacroModel Reference Manual - ISP

MacroModel Reference ManualChapter 4Chapter 4:Operation CodesThis chapter provides reference information for using the operation codes. Unless otherwisespecified, a zero in any opcode argument specifies the default value, if there is a default. Also,unless otherwise specified, the default is a reasonable value to choose if you do not have a goodreason to select a different value.4.1 File Reading and WritingREAD — READ a structureRead a structure from the input file. Repeated READ commands read multiple structures fromthe input file.arg1Molecular information retention0 Default behavior–1 Clear existing molecular information of previously read molecules and re-evaluatethe substructure information.This value is useful while using READ in BGIN–END loops and using ASL syntax in.sbc files (see ASL1, ASL2 and ASL3).–2 Clear existing molecular information of previously read molecules without re-evaluatingthe substructure information.WRIT — WRITe a structureWrites the current structure to the output file. WRIT is not necessary for Monte Carlo searchesand energy minimizations. It is used with molecular dynamics. Multiple WRIT statements putmultiple structures into the output file.TRED — Temporary file REaDReads a set of atomic coordinates from inname.tmp. This function is used to recover structuresfrom a failed MULT or MCMM run or when MULT is set in a multiple-loop MacroModelcommand file. In the latter case, all loops after the first must use a TRED rather than a READ.With Version 4.5 and later, the need for this command should be minimal, since updates arenow performed periodically during an MCMM search.MacroModel 9.7 Reference Manual 31