MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg3Note:arg4arg5arg6arg7arg8Surface-area derivative update frequencyThis is used in models 2 and 3. Default: 25 (new value in MacroModel 6.5) for PRCG,SD, and OSVM minimization modes and molecular dynamics, and 1 for FMNR andTNCG. Set to 1 or 2 for problem minimizations using SD, PRCG or OSVM; thedefault value cannot be overridden for FMNR and TNCG.Solvent polarization reset frequencyUses constant long range components except during resets. Default: 10.Minimum solvent/solute distanceUsed to remove overlapping solvent molecules in model 1. (Default: 2.5 Å)Flat-bottom positional constraint force constantUsed for restraining solvent molecules in model 1. (Default: 10. kcal/mol-Å 2 )Half-width of flat-bottomed positional constraintUsed for restraining solvent molecules in model 1. (Default: 2.5 Å)Maximum distance from solute centroidUsed in model 1. Molecules beyond this distance will have flat-bottomed constraintsas defined in arg6 and arg7. (Default 0.0 Å)LOGP — LOG P partition coefficient estimationThis command instructs the program to estimate the logarithm of the partition coefficientbetween two solvents, log P solv1,solv2 , for a series of molecules using the relationship:logP solv1,solv2 = ∆G solv2 – ∆G solv1( ) ⁄ ( 2.30RT)where P solv1,solv2 = [Solute] solv1 / [Solute] solv2 , ∆G solvN is the free energy of solvation of themolecule in solvent N, R is the gas constant, T is the temperature in kelvin. The first solvent,solv1, must be specified by an earlier SOLV command. The second solvent, solv2, is specifiedby arg2 as described below.LOGP must be followed by a BGIN/END loop containing appropriate READ, AUTO, and MINIopcodes. The AUTO opcode should set arg6 = 1.0000 for serial calculations and arg2 = −1 toavoid generation of lists of comparison atoms. Each molecule in the input file is minimizedtwice, once in each solvent. When LOGP calculation is enabled the behavior of subsequentREAD statements is modified and alternates between reading in new molecules and switchingMacroModel 9.7 Reference Manual 41