MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg1Frequency of writing to the filename-mon.mae structural data file1 Default. MacroModel writes to the filename-mon.mae file as frequently as it can forreal-time monitoring. For long jobs, this slows MacroModel execution.narg2Write the file only 1/n times as frequently as the default. Thus, arg1=10 wouldupdate the filename-mon.mae file 1/10 as frequently as the maximum rate.Recoloring of atoms in filename-mon.mae file0 No recoloring will be done.1 Atoms are recolored by energy gradient, an index of strain. A color scheme is usedthat follows the spectrum, where red indicates the most highly strained region of themolecule and blue indicates the most relaxed regions.4.2 Selection of Force Field, Nonbonded Cutoffs, andSolvation TreatmentFFLD — Force FieLD SelectionSpecifies a force field; there is no default for this command. A force field must be specified forenergetic calculations.The force-field files we supply have names fieldname.fld, where fieldname is one of: mm2,mm3, amber, amber94, oplsa, f10 or f11. MacroModel first looks in the local directory for thespecified force-field file and, if it is not found there, looks in the ~/.schrodinger/macromodel directory. If MacroModel does not find these files in either of these two locations,it finally searches in the $SCHRODINGER/mmshare-vversion/data directory. Before lookingfor fieldname.fld, MacroModel looks locally for a file called filename.fieldname (e.g.,my_job.amber). Under certain circumstances, other processes preparing jobs for running byMacroModel use this convention.arg1Force field1 MM2*. Allinger’s 1987 parameter set with many additions [1, 2]. Used for simpleorganics. Differs from the authentic field by use of a Coulomb’s law treatment ofelectrostatics and torsional barrier treatment of conjugation.2 MM3*. Allinger’s 1990 parameter set with additions [3]. Used for simple organics.Differs from the authentic field by use of a Coulomb’s law treatment of electrostaticsand torsional barrier treatment of conjugation.MacroModel 9.7 Reference Manual 33