Molecular simulations, AMBER

Some of the more approximate or specialized FFs encountered in the literature include CFF, CHEM-X, COSMIC, CYFF, DREIDING, MMX, SHAPES, TRIPOS, VALBOND, and UFF. Well-known FFs for modeling proteins and nucleic acids include AMBER, CHARMM, ECEPP, GROMOS, OPLS and their variants. Some of these latter FFs compromise the quality of reproducing subtle intramolecular electronic effects for the sake of being fast enough to treat biomacromolecules in long molecular simulations. 

Sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and OPLS force fields. PROQUANTUM for semiempirical (MOPAC) and ab initio (CADPAC) calculations via a graphical interface. 

Tel. 703-658-4854, fax 703-658-4887, e-mail syazdi presto.ig.com Desktop molecular modeling. NEMESIS SAMPLER for simple modeling. PRO-EXPLORE for sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and BOSS via a graphical interface. PRO-QUANTUM for semiempirical (MOPAC, extended Hiickel) and ab initio (CADPAC) calculations via a graphical interface. FDCALC and ESCALC for electrostatics calculations. N-DEE for analysis of NMR data. PC-PROT-I- (sequence analysis), PC-TAMMO-I- (protein—lipid modeling), and MASCA (statistics). Macintosh, PCs, and UNIX workstations. 

Tel. 358-0-4572378, fax 358-0-4572302, e-mail leif.laaksonen csc.fi Analysis of molecular simulation trajectories for CHARMM, Discover, YASP, MUMOD, GROMOS, and AMBER. Interface to ICONS for extended Hiickel calculations and to VSS for electrostatic potentials. 2D graphics of surfaces and electron density and orbitals. Silicon Graphics. 

The success of any molecular simulation method relies on the potential energy function for the system of interest, also known as force fields [27]. In case of proteins, several (semi)empirical atomistic force fields have been developed over the years, of which ENCAD [28,29], AMBER [30], CHARMM [31], GRO-MOS [32], and OPLSAA [33] are the most well known. In principle, the force field should include the electronic structure, but for most except the smallest systems the calculation of the electronic structure is prohibitively expensive, even when using approximations such as density functional theory. Instead, most potential energy functions are (semi)empirical classical approximations of the Born-Oppenheimer energy surface. 

Many different force fields are now available from commercial and other sources. Some force fields like the MM series of force fields developed by Allinger and the Merck MM [10] have been parameterized primarily for molecular mechanics and dynamics of small molecules. Due to their limited importance for polymer simulations, they will not be covered in this section however, they have been used to study conformational properties of model compounds for some aromatic polymers. In some cases, force fields primarily developed for biomolecules such as AMBER, CHARMM, and GROMOS have been used in the molecular simulation of polymeric systems. Force fields having particular importance for polymers include simple but versatile... 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

The GROMOS (Groningen molecular simulation) force field has been developed by Berendsen et al. for proteins and nucleic acids (see GROMOS Force Field). It is based essentially on the same formula for energy calculations as the AMBER force field ... 

Molecular dynamics simulation package with various force field implementations, special support for AMBER. Parallel version and Xll trajectory viewer available. http //ganter.chemie.uni-dortmund.de/MOSCITO/... 

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