MacroModel Reference Manual - ISP

Chapter 1: Capabilities and New Features• Novel method for accurate electrostatic and GB energies despite truncation of nonbondedinteractions. Implementation of the “Bond Dipole Cutoff” (BDCO) algorithm allows forexclusion of distant pairs from the nonbonded pairlist without compromising the absoluteaccuracy of the electrostatic and GB energies of a system. Much better agreement isachieved with the values of these energetic terms as calculated without cutoffs when BDCOis used as opposed to traditional residue-based cutoffs. Additionally, BDCO offers muchbetter energetic accuracy than residue-based cutoffs using default cutoff values despitethe fact that the BDCO calculation uses significantly fewer nonbonded pairs. Performanceis maintained while accuracy is significantly improved. See the BDCO opcode descriptionin this manual and Section 2.4 of the MacroModel User Manual for details.• Dihedral driving for production of Ramachandran-style energy surfaces. The non-drivendegrees of freedom for each point on the surface may be taken either from the mostrecently minimized structure or else from the starting structure.• In force-field substructures, parameters may be given a geometric dependence on valuesof torsions, angles or ring size. This geometric dependence is retested at key points in asimulation, such as the start of a new step of conformational search.• Ability to turn off interactions between sets of atoms. The sets are defined with the ASETcommand, and interactions are turned off with the ASNT command.• VDWB command replaces bend interactions with van der Waals interactions, for modelingtransition-metal complexes using the “points-on-a-sphere” model.• In addition to harmonic constraints on atomic positions (FXAT), distances (FXDI), angles(FXBA), and dihedral angles (FXTA), we provide support for fully “frozen” atoms: atomsthat do not move at all, but whose effect is felt by the atoms that can move. This isencoded by specifying a negative force-constant in a FXAT command.Note:Starting with MacroModel 6.0, there were changes in the way simultaneous FXAT andSUBS commands are handled. See the SUBS command description on page 64.• OPLS* and OPLS_2001 force fields now include short-range purely repulsive potentialson the polar hydrogen atoms. These potentials do not significantly affect the energies ofnormal structures but prevent catastrophic close approaches by negatively changed atomsin highly strained conformations such as those generated in aggressive conformationalsearch methods such as MCMM, LMCS, and LMC2. This modification is not needed for theOPLS_2005 force field, which uses Lennard-Jones 12-6 potentials for interactionsinvolving such atoms.MacroModel 9.7 Reference Manual 3