Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation.

  title={Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation.},
  author={Michael Feig and B. Montgomery Pettitt},
  journal={Journal of molecular biology},
  volume={286 4},
Hydration around the DNA fragment d(C5T5).(A5G5) is presented from two molecular dynamics simulations of 10 and 12 ns total simulation time. The DNA has been simulated as a flexible molecule with both the CHARMM and AMBER force fields in explicit solvent including counterions and 0.8 M additional NaCl salt. From the previous analysis of the DNA structure B-DNA conformations were found with the AMBER force-field and A-DNA conformations with CHARMM parameters. High-resolution hydration patterns… CONTINUE READING


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