Force MacroModel

The program MacroModel contains many modified versions of other force fields, e.g., AMBER, MM2, MM3, OPLSA. ... 

Macromodel (ref. 114) using the MM2 force field. Overlay of generated energy minimized conformations was done using SQ (ref. 115). 

Analysis of energy-minimized conformations generated using a 1000-step Monte Carlo conformational search with the AMBER force field by use of a MacroModel (version 3.5) demonstrates that both the benzothiazole ring and the carboxylic acid moieties of carbapenem 7 could be overlapped with those of 3-benzothiazolethiocephem <1997BMC601>. 

Molecular modeling with an AMBER-like and MM2 force fields. Batch conformational searching with BAKMDL. Interfaces to AMPAC, MacroModel, GAUSSIAN86, SYBYL, PCMODEL, CHEM-3D. VAX. 

The structure of daphmanidin B (67), C25H36NO6, was elucidated by 2D NM R data to possess a l-azabicydo[5.2.2]undecane moiety, like daphnezomines F and G [46]. The relative stereochemistry was deduced from NOFSY correlations. The conformation of the unit (C-2-C-5, C-18 to C-2, C-19, and N) in the l-azabicyclo[5.2.2]undecane moiety, with a twist-chair form as shown in Figure 18.16, was consistent with the results of a conformational search using MMFF force field [60] implemented in the Macromodel program [59]. 

Through molecular simplification, Norte et al determined that the presence of the flexible side chain was essential for the cytotoxic activity. It was further postulated that the conformation of the C14-C19 side chain was at least partially responsible for the variation in biological responses among the analogues. In order to verify this hypothesis, the stable conformations for all the compounds were determined using calculations that involved a multiconformer search using the Monte Carlo program in Macromodel and MM2 force fields [18]. 

Conformational analysis was performed for serotonin and 2-methyl serontonin varying tau 1 and tau 2 at 15 degree increments. For each conformation all other coordinates were optimized using MacroModel/BatchMin Version 3.1 with a modified MM2 force field (C. Still, Columbia University). 

The most rigorous dielectric continuum methods employ numerical solutions to the Poisson-Boltzmann equation [55]. As these methods are computationally quite expensive, in particular in connection with calculations of derivatives, much work has been concentrated on the development of computationally less expensive approximate continuum models of sufficient accuracy. One of the most widely used of these is the Generalized Born Solvent Accessible Surface Area (GB/SA) model developed by Still and coworkers [56,57]. The model is implemented in the MacroModel program [17,28] and parameterized for water and chloroform. It may be used in conjunction with the force fields available in MacroModel, e.g., AMBER, MM2, MM3, MMFF, OPTS. It should be noted that the original parameterization of the GB/SA model is based on the OPLS force field. 

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