Amber program

The Amber program of Professor Peter Kollman, University of California, San Francisco webpage... 

This chapter reviewed some of our group s contributions to the development and application of QM/MM methods specifically as applied to enzymatic reactions, including the use of sequential MD/QM methods, the use of effective fragment potentials for reaction mechanisms, the development of the new QM/MM interface in Amber, as well as the implementation and optimization of the SCC-DFTB method in the Amber program. This last implementation allows the application of advanced MD and sampling techniques available in Amber to QM/MM problems, as exemplified by the potential and free energy surface surfaces for the reaction catalyzed by the Tripanosoma cruzi enzyme /ram-sialidasc shown here. 

The initial conformation of the P solvated in a box of ethanol molecules was built by the LEAP module of the AMBER program version 8.0 [54] with... 

Examples of united-atom protein force-fields for proteins are GROMOS87 and 96,21,48 CHARMM PARAM19,49 OPLS/UA (united atom)50 and the original force fields developed for the AMBER program.51 United atom force fields were developed to reduce the computer time required for molecular dynamics simulations by reducing the number of atoms. They are still... 

In the present systems, all the MD calculations were performed using the AMBER program [51] and the force field parameter set, parm99 [59], was used for all the molecules. The partial atomic charges of ectoine molecules were taken from our previous study [38]. The starting conformation of the zwitterionic form of M-Enk that we adopted was an x-ray structure in which the peptide backbone is extended [60],... 

Molecular Dynamics Calculations Using Karplus CHARMm and Kollman s AMBER Programs... 

The Importance of Electrostatic Interactions. A molecule with the high charge density of DNA requires special attention to the approximations used in the calculations. In particular, we were concerned about the effect that a finite cutoff would have on the ionic environment and on the DNA structure itself. To test the effect of the spherical cutoff, we repeated the simulation of mlp using the AMBER program 33) and AMBER... 

A-based scaling can also be performed on the individual empirical terms in the force field, including target internal coordinates and non-bonded parameters. For example, in the widely used AMBER program, X scaling is introduced as follows... 

Finally, some details of the simulations merit mention. Molecular dynamics simulations of an NVT ensemble of a solute molecule in an aqueous environment represented by about 200 water molecules were carried out at 298 K using the AMBER program [11], The time considered for the simulations was 2,000 ps with time steps of 0.1 fs. The first l,000ps were used to ensure that equilibrium was reached completely, and the last 1,000 ps were to store the configurations of the... 

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