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Molecular Dynamics Simulation Studies Of Dna And Proteins: Force Field Parameter Development Of Small Ligands And Convergence Analysis For Simulations Of Biomolecules, Anne Loccisano

Electronic Theses and Dissertations

In the first part of this dissertation, CHARMM force field parameters for DNA minor groove-binding polyamides were developed. The parameterization involved the subdivision of the polyamides into model compounds, which were calibrated against MP2/6-31G(d) data. To test the new parameters, fourteen 10 ns molecular dynamics crystal simulations have been carried out on a DNA/polyamide complex at low (113K) and high (300K) temperatures. Of the 18 helical parameters examined, only one (stagger) is found to be statistically significant from the crystal structure with a t-test at the 95% confidence level. For the high temperature, stagger is non-significant at the 97% confidence …