Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

Rodrigo Galindo‐Murillo1, Christina Bergonzo1, Thomas E. Cheatham1

1 Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 7.10
DOI:  10.1002/0471142700.nc0710s56
Online Posting Date:  March, 2014
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The last in a set of units by the same authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. The unit describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories. Curr. Protoc. Nucleic Acid Chem. 56:7.10.1‐7.10.21. © 2014 by John Wiley & Sons, Inc.

Keywords: nucleic acid chemistry; nucleic acid structure and folding; force field review; simulation setup and analysis; simulation protocols; sampling methods

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Table of Contents

  • Introduction
  • Selecting an Appropriate Molecular Mechanical Force Field
  • Setting Up a Nucleic Acid System with Explicit Water and Counterions for a Molecular Dynamics or Monte Carlo Simulation
  • Equilibrating Simulations with Explicit Solvent
  • Basic Protocol 1: Initial Simulations for Solvent Equilibration
  • Enhanced Sampling Methods
  • Analyzing the Results
  • Inexpensive Methods for Estimating Crude Relative Free Energy Differences
  • Summary
  • Acknowledgments
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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