AMBER forcefield

Force field

$E_{\mathrm{t}\mathrm{o}\mathrm{t}\mathrm{a}\mathrm{l}}={\sum }_{\mathrm{b}\mathrm{o}\mathrm{n}\mathrm{d}\mathrm{s}}{K}_r(r-r_{eq}{)}^2+{\sum }_{\mathrm{a}\mathrm{n}\mathrm{g}\mathrm{l}\mathrm{e}\mathrm{s}}{K}_{\theta }(\theta -{\theta }_{eq}{)}^2+{\sum }_{\mathrm{d}\mathrm{i}\mathrm{h}\mathrm{e}\mathrm{d}\mathrm{r}\mathrm{a}\mathrm{l}\mathrm{s}}\frac{V_n}{2}[1+\mathrm{c}\mathrm{o}\mathrm{s}(n\varphi -\gamma )]+{\sum }_{i<j}[\frac{A_{ij}}{R_{ij}^{12}}-\frac{B_{ij}}{R_{ij}^6}+\frac{q_i{q}_j}{ϵR_{ij}}]+{\sum }_{\mathrm{H}\mathrm{-}\mathrm{b}\mathrm{o}\mathrm{n}\mathrm{d}\mathrm{s}}[\frac{C_{ij}}{R_{ij}^{12}}-\frac{D_{ij}}{R_{ij}^{10}}]$

External links

• AMBER parameters

References

1. Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society 117 pp 5179 - 5197 (1995)
2. David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham, Steve DeBolt, David Ferguson, George Seibel and Peter 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", Computer Physics Communications 91 pp. 1-41 (1995)