Paper Citing NAMD - Abstract
Project, Elad; Nachliel, Esther; Gutman, Menachem
Parameterization of Ca+2-protein interactions for molecular dynamics simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1163-1169, MAY 2008
Molecular dynamics simulations of Ca+2 ions near protein were performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The simulations reveal major, force-field dependent, inconsistencies in the interaction between the Ca+2 ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca+2-carboxylates interactions. The simulations results were compared to experimental data, using the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate interactions were carried out, yielding new parameters which reproduce experimental data. (C) 2007 Wiley Periodicals, Inc.
