Unit

UNIT 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

  1. Thomas E. Cheatham III1,
  2. Bernard R. Brooks2,
  3. Peter A. Kollman3

Published Online: 1 NOV 2001

DOI: 10.1002/0471142700.nc0710s06

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Cheatham, T. E., Brooks, B. R. and Kollman, P. A. 2001. Molecular Modeling of Nucleic Acid Structure: Setup and Analysis. Current Protocols in Nucleic Acid Chemistry. 6:7.10:7.10.1–7.10.17.

Author Information

  1. 1

    University of Utah, Salt Lake City, Utah

  2. 2

    National Institutes of Health, Bethesda, Maryland

  3. 3

    University of California, San Francisco, California

Publication History

  1. Published Online: 1 NOV 2001
  2. Published Print: SEP 2001

This is not the most recent version of the article. View current version (26 MAR 2014)

Abstract

The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It 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.