AMBER all-atom force field

Ross and Hardin, however, applied FEP calculations to examine how internally bound monovalent cation size affects antiparallel G-DNA quad-ruplex in water. The initial coordinates for the complex were taken from an X-ray diffraction structure based on Williamson s model.276 The calculations were carried out with the AMBER all-atom force field for DNA. The calculated free ene results indicated that Na is favored by 5 kcal/mol over Li and that Na is favored by 13 kcal/mol over K. The preference of Na over Li supports the notion that for stabilization of the quadruplex to occur, the ion must fit into the cavity properly. However, the computed preference of Na compared to K did not agree with experimental results. The authors suggested a few possibilities for this disagreement that need to be tested. 

United Atom force fieldsare used often for biological polymers. In th esc m oleciiles, a reduced ii nm ber of explicit h ydrogen s can have a notable effect on the speed of the calculation. Both the BlOn and OPLS force fields are United Atom force fields. AMBER con tain s both aU nited and an All Atom force field. 

AMBER was first developed as a united atom force field [S. J. Weiner et al., J. Am. Chem. Soc., 106, 765 (1984)] and later extended to include an all atom version [S. J. Weiner et al., J. Comp. Chem., 7, 230 (1986)]. HyperChem allows the user to switch back and forth between the united atom and all atom force fields as well as to mix the two force fields within the same molecule. Since the force field was developed for macromolecules, there are few atom types and parameters for small organic systems or inorganic systems, and most calculations on such systems with the AMBER force field will fail from lack of parameters. 

Protein models can be classified broadly into two types all-atom if they describe every atom in the protein explicitly and coarse-grained if they group several atoms into one interactive site. All-atom force fields such as CHARMM [4], AMBER [5],... 

Reddy et al. used AMBER 3.0 and the all-atom force field to calculate relative solvation and binding free energies for a peptide inhibitor with HIV-1 protease. i The X-ray structure of HIV-1 protease complexed with Ac-Ser-Leu-Asn-(Phe-Hea-Pro)-Ile-Val-OMe (SI), where Hea is hydroxyethylamine, was used as the starting configuration. The Val residue of the inhibitor was mutated... 

Erion and Reddy used AMBER and the all-atom force field to calculate relative hydration free energies and relative binding free energies starting from... 

Rastelli et al.1 9 calculated relative free energies of binding for dUMP and dCMP to TS by means of AMBER 4.0, the all-atom force field, and the TS-dUMP complex crystal structure.224 The AAGlfi a muta-... 

Weiner, S.J. KoUman, P.A. Nguyen, D.T. Case, D.A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 1986, 7, 230, http //www.amber.ucsf.edu/amber/amber.litml. 

Molecular dynamics was performed at constant temperature with AMBER 4.1 all-atom force field [121] and Particle Mesh Ewald method (PME) was used for the calculation of electrostatic interactions [122]. This is a fast implementation of the Ewald summation method for calculating the full electrostatic energy of a unit cell in a macroscopic lattice of repeating images. The PME grid spacing was 1.0A. It was interpolated on a cubic B-spline, with the direct set tolerance set to 0.000001. Periodic boundary conditions were imposed in all directions. All solute-solute non-bonded interactions were calculated without jmy cut-off distance, while a non-bonded residue based cutoff distance of 9A was used for the solvent-solvent and for the solute-solvent interactions. The non-bonded pair list was updated every 20 steps and the... 

PCMODEL Version 8 became available in 2002. New features in version 8 include support for different and improved force fields along with the MMX, MM3, MMFF94, Amber, and Oplsaa force fields currently supported. The atom limit has been increased to 2500 atoms, and support for reading and writing PDB and SDF files has been added. Transition-metal complexes can be built with explicit sigma bonding, lone-pair coordination, and pi-system coordination. Parameters are available for all transition metals. 

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