Molecular modeling CHARMM

Figure 16.12 Chemical structure (a), and CHARMm molecular modeling picture (b), of the dendritic box [159]...

Figure 5 Conformers of the N-terminal decapeptide TTLTEPEPDL from the leech protease hementin. Molecular modeling predictions using Quanta/CharmM of two low-energy conformers.131...

Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates... 

Academia has been rich in producing theoretical computational methodology that underpins molecular modeling. The following software arose from universities or private and publicly funded institutes AMBER [10], INSIGHT [11,12], CHARMM [13], SYBYL [14], GRID [15], DOCK [16] and HINT (Hydropathic INTeractions) [39]. All except AMBER were commercialized. 

All of these programs are available for Unix operating system. Most of the Windows versions are incorporated into commercial molecular modeling packages such as MM in Chem3D of CambridgeSoft (http //www.camsoft.com), AMBER and CHARMm in HyperChem of HyperCube (http //www.hyper.com), and SYBYL... 

HyperChem is the PC-based molecular modeling and simulation software package marketed by Hypercube Inc. (http //www.hyper.com). The program provides molecular mechanics (with MM +, AMBER, BIO+ (CHARMm), and OPLS force... 

A model calculation for Type A molecules using the force-field method CHARMm (Chemistry in Harvard Molecular Modeling) showed a linear arrangement of the poly (ethylene glycol) chains for the compound 31a (Figure 6.5). 

Many of the aforementioned features are combined in integrated molecular modeling software such as SYBYL, Chem-X, COSMIC,80 Quanta and CHARMm, BIOGRAF, Insight and Discover, Chemlab, and MOLIDEA. These packages are available on a variety of hardware platforms ranging from personal computers (PCs) to mainframe computers. 

Molecular modeling package - Quanta and CharmM - Release 2.1 Polygen Corporation Waltham, USA, 1990. 

In this paper we develop a new method for finding the three-dimensional space that surrounds a substrate/ligand. This space, which is the chemical equivalent of the receptor, is represented as a protein structure, referred herein as a "pseudo-receptor". A variety of computational tools are used to create the pseudo-receptor. A molecular mechanics and dynamics program, CHARMm(l), is used to calculate the energy and conformational features of the pseudo-receptor. The program QUANTA(l) is used to define the preliminary protein sequence, secondary structure, graphically examine molecular interactions, interface with CHARMm, and model amino-acid mutations in the protein sequence. 

It is useful to point out that two sensitivity coefficients associated with parameters of the same type may give different sensitivities. For example, it is common in current biomolecular force fields to use the same force field parameter for chemically similar groups (e.g., the atomic partial charges for all the amide nitrogens have the same value in commonly used force fields such as those in the GROMOS, CHARMM, and AMBER molecular modeling packages). 

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