Software MacroModel

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. 

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. 

II. Product Summaries Schrodinger provides its FirstDiscovery software suite to address and aid in the discovery process in industry. First Discovery runs under Unix and Linux and it includes several programs Glide, Jaguar, Liaison, LigPrep, MacroModel, Maestro, Mopac 2002, pKa predictor, Phase, Prime, QikPro, Qsite, and Strike. For the Microsoft Windows platform Schrodinger offers CAChe, BioMedCAChe, ChemFrontier, MaterialsExplorer, QikPro, Titan, and WinMOPAC. 

T. Hendrickson, and W. C. Still, ). Comput. Chem. 11, 440 (1990). MacroModel— An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. 

Mohamadi F, Richards NGJ, Guida WC, Liskamp R, Lipton M, Caufield C, et al. MacroModel—An integrated software system for modeling organic and bio-organic molecules using molecular mechanics. 7 Comput Chem 1990 1 440-67. 

QikProp is a software [QikProp - Schrodinger, 2003] that calculates a set of 31 physico-chemical descriptors generated by using the program MacroModel [MacroModels - Schrodinger, 1990] for —> ADME property prediction of drug candidates. The list of QikProp descriptors is given in Table Ql. 

G. Chang, T. Hendrickson, and W. C. Still, J. Comput. Chem., 11, 440 (1990). MacroModel—An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. [The MacroModel software is available from W. C. Still, Department of Chemistry, Columbia University, New York, NY 10027, U.S.A.]... 

For those with an interest in true 3-D structures, we have also a number of user-friendly molecular modeling packages available on our system, among them SYBYL, from Tripos Associates, Inc., and Macromodel, from Prof. Clark Still, Columbia University. Both can be accessed via the Versaterm Pro emulation software on the Macintosh, as well as from intermediate and high-performance workstations like the NEC-APC and the Evans and Sutherland PS-300. These specialist packages are maintained by our Drug Design department, who help out users with the specifics of the software. 

Many such software packages are available. We have programs from commercial (CHEMX, Molecular Design Ltd), industrial (COSMIC, Dr. J. G. Vinter of Smith, Kline and French) and academic (MACROMODEL, Dr. Clark Still, Columbia University) sources. 

In this context, we would like to emphasize the often blurred distinction between force field , the functional form and parameters, and the computer program used. The force field used by Weiner et al. (often called the AMBER force field ) has been implemented within the TRIPOS, DISCOVER, and MACROMODEL programs. In principle, the Cornell et al. force field, because of its simple functional form, could be implemented within all the programs mentioned above, with only minor modifications required in a few cases. On the other hand, for example, AMBER could not, without major changes, implement the MM4 force field. In our opinion, force field parameters, in contrast to the software in which they are used, must be made available in their entirety when an article using them is published, either in the article or an appendix or through the World Wide Web. A publication is not really science unless its results can be reproduced by others ... 

For the various practical courses, the Department of Chemistry offers a computer-laboratory equipped with some 25 Silicon Graphics workstations. This laboratory is also accessible to students wishing to work on projects by themselves. All students, upon registration, obtain a user-ID which gives them access to the software installed on these workstations (MAPLE, MATHEMATICA, and application software used in courses such as UNICHEM, MACROMODEL, or GROMOS ), and to services such as electronic mail and the World Wide Web. 

Since the use of micromodels is too expensive and complicated for entire building analysis under seismic excitations and due to the fact that available software capabilities are often limited in handling such FE micromodels, equivalent FE macromodels are being used for practical seismic analysis of LB or NLB masonry constmction. 

A working model (Figure 154) based on the NMR results and routinely accessible calculations (AMBER force field, as implemented in the MacroModel software package) has been proposed. This model is based on two assumptions (1) the predominant rotamer around the bond between the benzylic C atom and the N atom is that in which the benzylic proton is eclipsed with the carbonyl group, and (2) one of the two nonhydrogen substituents at C(3) occupies the anti position, relative to the carbonyl group. 

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