MacroModel Reference Manual - ISP

Chapter 4: Operation Codes3 AMBER*. Kollman’s united atom and all atom fields with additional parameters fororganic functionality [4, 5]. Used primarily for biopolymers.4 AMBER94. Kollman’s 1994 version of AMBER, Amber4.1 [6].5 OPLSA*. Jorgensen’s nonbonded parameter set + AMBER bonded functions forliquid simulations [7]. Used primarily for peptides. Best for relatively rigid molecules,because the torsional parameters have not been optimized to reproduce conformationalenergy differences.10 MMFF94 and MMFF94s [8–14]. See also the description of arg4 of this command.11 OPLS_2001. This force field, developed by Professor W. Jorgenson of Yale University,is probably the best one available by default in MacroModel for condensedphasesimulations of peptides [15]. Formerly known as OPLS-AA.A value of 10 or 11 for arg1 encodes a force-field whose parameters are obtainedfrom a coprocess interacting with MacroModel using the BMFF mechanism. SeeAppendix E for details. The force-field file name used in this case is f10.fld forMMFF and f11.fld for OPLS_2001.14 OPLS_2005. An enhanced version of the OPLS_2001 all-atom force field developedby Schrödinger to provide a larger coverage of organic functionality. In particularall torsional parameters have been refit to reproduce the conformationalenergetics derived at a higher level of quantum theory and additional charges havebeen fit to support additional organic functionality. The parameters for proteins havebeen updated to the ones published more recently [52].arg2Electrostatic treatment0 Default. Uses dielectric treatment encoded within force field file unless solvationmodel 3 is used (see SOLV command), in which case the constant dielectric treatmentis used.Note:All our force fields are supplied, by default, with constant dielectric electrostatics.Prior to MacroModel 6.0, AMBER*, MM2, and MM3 used distance-dependentdielectric constant by default.–1 Turns Coulombic molecular electrostatics off.1 Gives constant dielectric electrostatics.2 Gives distance-dependent dielectric electrostatics.34MacroModel 9.7 Reference Manual