MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg3Frequency of updating a conformational searchWhen an update is performed, the following actions take place:• The current .tmp file is removed, and structures that are to be saved (based on thevalue of the current global energetic minimum) are written to the output file.• A summary of the progress of the search so far is written to the log file.• Ifajobname.upt file is created in the directory from which the job was initiated, anupdate is performed immediately, in addition to those specified by arg3.0 Default: Perform an update every tenth of a run, but not more often than every tensteps nor less often than every 500 steps.narg4Perform an update every n steps.LMCS serial job0 Not an LMCS serial job. A single low-mode search is performed, with all input structurestreated as seed structures, as if found in previous iterations.Note:≠0arg5arg4=0 is unsuitable for non-conformers.LMCS serial job; this implies that a separate conformational search will be performedfor each structure in the input file. This takes advantage of the ability ofLMCS to define fruitful search directions without specification of variable torsions.An LMCS serial job can be run only when there are no commands specifying atomnumbers—such as TORS or CHIG—which might translate to incorrect specificationsin the different input structures.Probability of taking a TORS/MOLS step0 If this is an LMCS job, all steps will be LMCS steps.narg6If this is an LMCS job and there are TORS or MOLS commands present, this fractionof moves will be TORS or MOLS (i.e., not LMCS) moves.Maximum number of conformers to write to the output structure file for eachsearch performedFor example, in a serial search, the search for each input structure would produce atmost the number of structures specified here.Using a value other than 0 or 1 for this argument is not permitted in a ligpreplicensed calculation where only one output structure is permitted per structureprocessed.104MacroModel 9.7 Reference Manual