MacroModel Reference Manual - ISP

Chapter 4: Operation Codes4 Rotate by 180 degrees about the first principal axis and then rotate by 180 degreesabout the second principal axis.5 Generate all 4 alignments with respect to the principal axis and write each alignmentto the output structure file.4.10 Conformational SearchingThe entire contents of the input file are used as the “seed” for the search for most searchmethods. At the start of a run, the full contents of this file is read, and the search proceeds as ifall the structures in the input file had been found in the current search. This allows a new searchto use the results of a previously run, partial search as its input. Of course, for a new search, theinput file will contain a single structure.The output file from the search contains in the header lines of the individual structures thenumber of times each structure was found. Therefore, the full benefits of usage-directednessare obtained in a subsequently run search. This degeneracy information is ignored, for technicalreasons, during a network-distributed search. In a distributed search, or in any searchseeded from an output file produced by an earlier version of MacroModel, the structures aretreated as if they each occurred exactly once in a previous search. Debug (DEBG) flag 360, ifset, instructs the program to ignore the degeneracy information even if it would otherwiseutilize it.Searches may be updated during program execution. When a search is updated, the informationin the temporary file (filename.tmp) is written to the output file, after discarding structuresthat are not within the specified energetic window of the current global minimum. A summaryof the job progress is also printed, which includes information on the number of times variousstructures were found and the convergence of these structures during minimization. Asdescribed in Chapter 2, updates can be initiated interactively by the user. Automatic, periodicupdates can be controlled with the MCOP command.For a discussion of conformational search protocols, see the Chapter 9 of the MacroModelUser Manual. As discussed there, it is advisable to perform the search without exhaustiveminimization of all found structures and to subsequently reminimize the surviving structures.This can be done without initiating a new MacroModel job, by inserting into the .com file aRWND command following the MINI command that terminates the search setup, then insertinga BGIN/END loop within which a READ/MINI sequence is specified. The COMP atoms used inthe search will continue to be active during the reminimization.The maximum number of conformations that can be stored when using MCMM, LMCS, SPMC, orMULT is no longer limited to 10000. See the respective command descriptions and Section 1.4on page 9 for further details.MacroModel 9.7 Reference Manual 83