MacroModel Reference Manual - ISP

Chapter 1: Capabilities and New Features• BMFF (BatchMin Force-Field inter-process-communication library) allows an externalprocess to generate force-field parameters and pass them to MacroModel. SeeAppendix E for details. This mechanism was used to implement MMFF, using a co-processsupplied by Dr. Thomas A. Halgren; however, the mechanism is general and shouldgreatly simplify the porting of additional force fields to MacroModel.• Analytical continuum treatment of solvation (water, chloroform, and octanol setup filessupplied). For precise parameter matching, it is possible to specify atomic connectivityout to the beta-atom level in .slv files.• Ability to specify multiple parameter blocks in the solvation files for use with differentforce fields. This is done by placing a force-field number on an SMODEL line of the file. Ifan SMODEL block is found containing both the force field and the solvation model specifiedin the .com file, that block is used. If no block is found specifying the current forcefield, then, if a block is found for the current model specifying 0 for the force field, thisblock is used as the default. If neither is found, the first SMODEL block for the solvationmodel specified in the .com file is used. The program can also be instructed to use thegeneral set of parameters for a particular solvent using arg2 of SOLV. Parametrizations forspecific force fields are provided for OPLS-AA and MMFF for water and octanol.• GB/SA with fixed/frozen atoms. We have continued to improve the use of both the GBand the SA parts of GB/SA when fixed and/or frozen atoms are in use. The intent is toprovide speed optimization with minimal loss of accuracy. For energetic calculations, frozenatoms need not “see” each other; thus, for example, frozen nonbonded pairs aredeleted from the nonbonded pairlist. However, the motion of the moving atoms causes theGB radii of the frozen atoms to change, and the GB energy contributions of frozen atompairs will then change accordingly. To accommodate this without losing all the advantageof frozen-atom optimization, starting with MacroModel 7.0 we define a cutoff, CUTFMM,which defines a radius around the moving atoms within which any frozen atoms aretreated as moving for the purpose of GB only. This is specified in arg8 of the EXNB command.Similar concerns arise for SA, where a CUTSFM is defined in arg5 of EXN2, anextension of the EXNB command.• Correction for Born radii when not all nonbonded pairs are included in a calculation. Forcalculations on large systems such as proteins, typically not all nonbonded interactionsare included in energetic and derivative calculations, to make simulations tractable. Thisleads to systematic errors in the values of Born radii used to calculate the GB energy inthe GB/SA solvation model. A correction is done to account for this error and improveenergetic and derivative calculations. See Section 2.3 of the MacroModel User Manualfor further details.• Vacuum, constant dielectric and distance-dependent-dielectric solvation treatments.2MacroModel 9.7 Reference Manual