MacroModel

The MacroModel program of Professor C Still, Columbia University webpage... 

The generalized Born/surface area (GB/SA) model is a combination of the Born and SASA models. This method has been effective in describing the solvation of biomolecular molecules. It is incorporated in the MacroModel software package. 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

The preeminent offerings in this crowded market include MacroModel (Columbia University, New York), Insight (Biosym Technologies,... 

Branching in PVC has been suggested as a possible source of instability for a long time. 2-methyl-2-chloro-propane and 3-ethyl-3-chloropentane are much less stable than the corresponding secondary chlorine compounds [31]. Comparison of 3-chloro-3-ethylpentane with 3-chloro-4-ethylhexane showed that the latter was by far the most stable [32]. Macromodels containing ter-... 

MacroModel V3.5X (1992) Interactive molecular modeling system. Department of... 

Compared with the use of arbitrary grid interfaces in combination with reduced-order flow models, the porous medium approach allows one to deal with an even larger multitude of micro channels. Furthermore, for comparatively simple geometries with only a limited number of channels, it represents a simple way to provide qualitative estimates of the flow distribution. However, as a coarse-grained description it does not reach the level of accuracy as reduced-order models. Compared with the macromodel approach as propagated by Commenge et al, the porous medium approach has a broader scope of applicability and can also be applied when recirculation zones appear in the flow distribution chamber. However, the macromodel approach is computationally less expensive and can ideally be used for optimization studies. 

Monte-Carlo conformational analysis of the peptidomimetic perhydropyrazino[l,2-tf]pyrimidine 32a was performed using the MacroModel V 6.0 program <1999JA12204> and for 32 (R = H R" = (CFl2)2Ph, R " = Bu Y= (CH2)2C6H4-OH-/>) using MacroModel V7.1 <2002JME1395>. 

Mohamadi, F Richards, N. G. J., Guida, W. C Liskamp, R., Lipton, M., Caufield, C., et al. (1990) MacroModel an integrated software systems for modeling organic and bioorganic molecules using molecular mechanics. J. Comput. Chem. 11,440-467. 

MM3-94 calculations for this work (including parameters for the NO2 group). cCalculated for this work with MacroModel 5.0 implementation of AMBER. 

T. Bechthold, E.B. Rudnyi, J.G. Korvink, M. Graf, and A. Hierlemann. Connectingheat transfer macromodels for MEMS-array stmctru es . Journal of Micromechanics and Microengineering 15 (2005), 1205-1214. 

Fig. I. (Left) Numbering of vinblastine-type alkaloids in this chapter according to the biogenetic scheme of LeMen and Taylor (134), with equivalent atoms in all synthetic intermediates equally labeled. (Right) Approximation of computer-generated, energy-minimized structure, obtained with the Clark Still MACROMODEL program.

We thank Professor J. L6vy for providing us with copies of Refs. 124 and 125. We also thank Professor Clark Still for a gift of the MACROMODEL computer program. Our research was supported by grant ROl-12010 from the National Cancer Institute. 

Calculations by T. D. Spitzer of our group at the University of Vermont using the MACROMODEL program. 

Some results on the molecular modeling of N,N -di-methylxYlaramide (1) and IV lV -dihexYlxylaramide (2) using MacroModel V.2 are presented. Nine minimized conformers were considered and their populations calculated. Average 2 3 3 4 were then calculated and those values... 

Theoretical coupling constants for individual rotamers were obtained directly from MacroModel employing an empirical generalization of the Karplus Equation ( ). Calculated average couplings came from the expression ... 

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