MacroModel, molecular structure

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. 

To cortfigrrre it, right-click on the node and in the dialog box that opens select the file where the molecular structures are available here, we will choose the example molecules already loaded in directory at SCHRODINGER/macromodel-ligprep/ samples/examples/1 Ssmiles.smi. 

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 goal of the present study was to develop a computer-based cubic section model of the substrate binding domain of HLADH. It was considered that the Jones cubic section model could be refined by use of computer assisted substrate overlay in combination with kinetic data on a wide variety of substrates. As in the Jones approach we used the alcohol products as the surrogate substrate structures. Thus, we determined the low energy conformation of alcohols produced from ketones that have been reported to be reduced by HLADH and for which comparative kinetic data vs cyclohexanol could be calculated. As well, we determined the preferred conformations of all alcohols that would have been produced from ketones subjected to but failing to undergo HLADH reduction. These calculations utilised molecular mechanics (MACROMODEL) and yielded accurate co-ordinates for ali atoms in each alcohol. Where enantiomeric or stereoisomeric alcohols were produced or capable of production, the co-ordinates of each were calculated. 

Recently, we proposed a new bioactive conformation of paclitaxel, RKDOR-Taxol [50], based on (i) the 19F-13C distances obtained by the REDOR experiment [49], (ii) the photoaffinity labeling of microtubules [51], (iii) the crystal structure (PDB code 1TUB) of the Zn2+-stabilized aP-tubulin dimer model determined by cryo-electron microscopy (cryo-EM) [52], and (iv) molecular modeling (Monte Carlo Macromodel) [50], In this computational biology analysis, we first docked a paclitaxel-photoaffinity label molecule to the position identified by our photoaffinity labeling study and then optimized the... 

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. 

PCMODEL also reads and writes files imported from many other types of molecular calculation programs (including MM2, MM3, MOPAC, Gaussian, Macromodel, Alchemy, Sybyl, and Chem-3D), so you can create and edit your preferred structure calculation files. Alternatively, you can use the PCM file format, an easily readable, free-format file that maintains all structure information including substructure names and membership, atomic charge, and user-specified minimization parameters. Since these files are ASCII text files, they can be transferred to another computer as input to calculations on another system. 

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