Software CHARMM

Other Popular Force Fields and MM Software. CHARMM, OPLS, and GROMOS... 

California), Sibyl (Tripos, Missouri), ChemX (Chemical Design, UK), BioGraf (Molecular Simulations, California), Charmm/Quanta (Polygen Corp., Massachusetts), PC Model (Serena Software, Indiana), ChemLab (ChemLab Inc., Illinois), and a large number of personal computer-based packages. 

The GEMM software on the ST-100 is not a stand-alone package, and it requires a front-end simulation software package that runs on the host to provide data and to send command requests. It was designed and written with CHARMM (Chemistry at HARvard Macro-molecular Mechanics) (14) as the primary front-end, but additional software packages, such as AMBER (15), have subsequently been modified to drive GEMM. 

The current implementation is best with CHARMM as a front-end, though other software packages have been modified to drive GEMM. 

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. 

We thank J. Apostolakis and Professor A. Pluckthun for helpful discussions. The calculations were performed on an SGI Indigo2 and an eight-processor SGI Challenge (R4400 processors). The CHARMM program within the version 4.0 of the QUANTA software package (Biosym-MSI Inc) was used for some of the minimization performed in this work. The CCLD program is available from A. Caflisch. 

Version of CHARMM somewhat extended and made available in Acccirys software products. 

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... 

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. 

PCMODEL are supported by developers at Columbia University and Indiana University, respectively. Neither is backed by a large marketing or sales force. Yet each has enjoyed noteworthy success in terms of being used in publications. Also plotted are CJACS hits of Chemical Design Ltd., which supports Chem-X, and Serena Software, which has PCMODEL. Literature mention of the Chem-X package exceeded that of Insight/Discover, SYBYL, and Quanta/CHARMm for at least one year in the 1980s, but publications from users of Chem-X have not kept up and have fluctuated around the same level in the last few years. 

CHARMM, AMBER, GROMOS, GROMACS, Discover, and VMD/NAMD are some programs used widely to perform MD simulations (http //cmm.cit.nih.gov/modeUng/software. html). 

There are several MM force fields available, such as OPLS [29], CHARMM [30], AMBER [31], GROMOS [32], MMFF [33], CVFF [34], to mention a few. Several of them have been combined with the QM calculation programs and used in the combined QM/MM molecular dynamics simulations. [12,15,35,36] In our own work we have combined either GAUSSIAN94 [24] or GAMESS [25] with our own simulation software which is the modified version of McMOLDYN [37] package to study solvation phenomena and radical systems [38,39]. 

Fig. 22 The molecular shape of tetramer with a Cn spacer unit shows the minimized structure in the gas phase at absolute zero using a Silicon Graphics system operating with Quanta and CHARMm software...

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