Software Amber

X-ray crystallographic analysis Modeling software, AMBER, UniChem, VAMP, RS Discovery database system, products of CAChe Scientific, Health Designs (TOPKAT), IntelliGenetics, Genetics Computer Group (GCG)... 

Modifications of the various versions of the AMBER parameter sets are implemented in numerous commercial and academic software packages. They are often referred to as AMBER. In every case, the user should read the documentation provided critically, and check the implementation by comparing the results of the implementation with original data. 

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 free energy calculations with complexes of oligomeric DNA with distamycin and netropsin presented in this chapter were carried out using the AMBER force field2 and the AMBER software.21 The associated potential energy function is ... 

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. 

Sometimes referred to as AMBER force fields new versions are first coded in software of that name. All-atom (AA) and united-atom (UA) versions exist. 

The first molecular mechanics studies of alkali metals were of the Na+, K+, Rb+ and Cs+ complexes of 18-crown-6 (Fig. 14.1)12551. The AMBER software system was used and the M+... 0 interactions were modeled using a combination of van der Waals... 

An introduction to the modeling methods can be found in refs. [22,231. The classical MD simulations reported here were performed with the modified AMBER software/241 in which the potential energy consists of harmonic deformations of bond and angles, dihedral energies, plus non-bonded interactions represented by a sum of pair wise additive coulombic and van der Waals contributions ... 

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... 

VIBRATE (normal modes), VOID (protein packing), and mdXvu (visualization of AMBER trajectory files). QCPE has also accepted the responsibility to distribute semicommercial academic software, such as MM2, MM3, MOPAC 93, POLYRATE, PEFF, and COMPARE-CONFORMER. Most programs in library are in FORTRAN and are available as source code. Current catalogs and information are available by anonymous ftp from qcpe6.chem.indiana.edu (129.79.74.206). Many of the programs run on several hardware platforms, including DEC VAX, IBM, Silicon Graphics, Stardent, Sun, Fujitsu, and Cray. 

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]. 

---