Extending the AMBER Force Field to Describe Fluorescent Probes

Faculty Mentor(s)

Dr. Brent Krueger, Hope College

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We are developing a method for studying the structural dynamics of biomolecules, which couples fluorescence spectroscopy and computational modeling, providing a more complete understanding than is possible with either technique alone. The computational modeling will be based primarily on molecular dynamics (MD) simulation. Before running MD, dye parameters were determined that are consistent with the Cornell et al. force field (1995, J. Am. Chem. Soc.) and the generalized AMBER force field (GAFF; Wang et al., 2004, J. Comput Chem.) commonly used in AMBER. Parameterization was carried out using quantum mechanical calculations to determine low-energy conformers of the dyes and to calculate electrostatic potentials for these conformers. The RESP charge fitting procedure was used to derive atomic charges. All other parameters were assigned by analogy to pre-existing force field parameters. Several DNA- and RNA-fluorescent probe systems will be explicitly solvated in water and equilibrated before beginning production MD simulations. These simulations will be used to generate simulated fluorescence data for direct comparison to experimental bulk and single-molecule FRET data.


This research was supported by the National Science Foundation RUI, MRI, REU, & CIEG programs, the Howard Hughes Medical Institute, the ACS-Petroleum Research Fund, the Midwest Undergraduate Computation Chemistry Consortium, and Teragrid Cyberinfastructure.

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