MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg3Hydrogen bonding treatment0 Uses equation selected in force field file (default).1 Turns off explicit 10,12 hydrogen bonding function and uses 6,12 Lennard Jonesinstead.2 Gives explicit 10,12 hydrogen bonding function.arg4arg5arg7BMFF force-field optionFor a BMFF force-field, this requests a special option given in an “Option:” line ofthe MacroModel force-field file. For MMFF, a “1” in this position requests thatMMFFs parameters be used; these enforce planarity about delocalized sp2nitrogens.Molecular dielectric constantDefault = 1.0. The solvent dielectric constant is normally read from the solvent file(see SOLV command) and should not generally be set here.Planarity of aromatic ringsEnforce planarity of aromatic rings for OPLS_200X force fields.0 Do not enforce planarity of aromatic rings. This is the default.1 Enforce planarity of aromatic rings.arg8Coefficient for torsional dampingDefault: 100.For highly strained conformations in which bond angles become straight, relateddihedral angles can become undefined. To avoid this problem and the physicallyrapidly varying dihedral angle potentials for states close to this, the torsional potentialis damped using the function:f damp = (1 − exp(−c tors (1−cos 2 θ 1 ))) (1 − exp−c tors (1−cos 2 θ 2 )))where θ 1 and θ 2 are the bond angles formed by the first and last three atoms in thetorsional potentials.The default value of the torsional damping coefficient, c tors , of 100 damps the dihedralangle potential significantly for bond angles less than 10 degrees and workswell. This argument permits one to change the value of c tors . Increasing c tors dramaticallyreduces the range over which the damping is applied.MacroModel 9.7 Reference Manual 35