Amber Simulants

AMBER simulations (in TIP3P explicit solvent model [76]). As such, in terms of speed and efficiency, our GBEMP model underperforms medium-resolution MARTINI model by the factor of about 2 [77] but it can outperform high-resolution PRIMO CG model by the factor of about 2 [36],... 

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/... 

Lsc th e force fields th at have dern on strated accuracy for particu lar molecules or simulations. For example, CiPLS reproduces physical properties in liquid simulations extremely well. MM+ reproduces the structure and thermodynamic properties of small, nonpolar molecules better than AMBER, BIO+, and OPLS. 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

Another difference between the force fields is the calculation of electrostatic interactions. AMBER, BIO+, and OPLS use point charges to model electrostatic interactions. MM+ calculates electrostatic interactions using bond dipoles. The bond dipole method may not adequately simulate very polar or charged systems. 

Heat is used to darken amber, ivory, and jade to simulate age. Pieces of amber and tortoiseshell can be reconstmcted, ie, joined under heat and moderate pressure. By careful heating in oil, milky amber can be clarified when the gas and water within small bubbles diffuse out of the stone. If heating is rapid, the attractive sun-spangle cracking shown in Figure 1 results. 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

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. 

Case DA et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16) 1668-1688... 

PPII helix-forming propensities have been measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and T. P. Creamer (unpublished results). In the simulations the peptide backbone was constrained to be in the PPII conformation, defined as (0,VO = ( — 75 25°, +145 25°), using constraint potentials described previously (Yun and Hermans, 1991 Creamer and Rose, 1994). The AMBER/ OPLS potential (Jorgensen and Tirado-Rives, 1988 Jorgensen and Severance, 1990) was employed at a temperature of 298° K, with solvent treated as a dielectric continuum of s = 78. After an initial equilibration period of 1 x 104 cycles, simulations were run for 2 x 106 cycles. Each cycle consisted of a number of attempted rotations about dihedrals equal to the total number of rotatable bonds in the peptide. Conformations were saved for analysis every 100 cycles. Solvent-accessible surface areas were calculated using the method of Richmond (1984) and a probe of 1.40 A radius. 

D. M. Ferguson, G. L. Seibel, and P. A. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comp. Phys. Comm. 91 1 (1995). 

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