MacroModel Reference Manual - ISP

Chapter 4: Operation CodesParametrizations specific for OPLS-AA and MMFF(s) have been added to the water.slv filefor model 3. Other force fields continue to use the default parametrization which is unmodifiedfrom previous releases. The default parametrization in the octanol.slv file was constructedfor the MMFF force field. As well, a parametrization specific for OPLS-AA is present in theoctanol.slv file. The new parameters for MMFF are based on the parametrization describedin [19] for water, and in [20] for octanol. We gratefully acknowledge C. H. Reynolds’s assistancein utilizing these parameterizations. Available force field specific parameterizations areused by default unless the program is instructed otherwise (see arg2 below).Calculations with solvation use periodically updated constant area and/or polarization derivativesto speed the calculation. Default update frequencies are given below. These frequenciescan be changed via arg3 and arg4. If difficulties in achieving low gradients are found or ifdynamics in solvent is unstable, reduce these numbers (e.g., to 2). Energy minimizations andmolecular dynamics simulations using continuum solvation models 2 and 3 run approximately1/2–1/4 the rate of in vacuo calculations.Note:MacroModel carries out energy minimizations with an analytical, approximate functionfor surface areas. Thus, intermediate energies reflect the approximate function.The final energies reported, however, use an accurate numerical function. Thus, intermediateand final energies will differ.It is recommended that the EXNB opcode be used in conjunction with solvent model 3 (GB/SA)and that the electrostatic cutoff distance be set to 20 Angstroms.arg1Solvation model2 Total solvation based on approximate solvent accessible surface areas (Scheraga’sparameters).3 GB/SA Solvation Model. Cavity and Van der Waals components from approximatesolvent accessible surface areas, and electrostatic (polarization) component fromGB mode. See Still et al. [18] for a discussion of effective Born radii calculation.This is the best solvent model to use.arg2SolventIf arg2 < 0 use the general parameterization from the .slv file rather than theparametrization for the specific force field.1, −1 Water (models 2 and 3)5, −5 CHCl 3 (model 3)9, −9 Octanol (model 3)40MacroModel 9.7 Reference Manual