UNIT 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis
Published Online: 1 NOV 2001
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
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.
- Published Online: 1 NOV 2001
- Published Print: SEP 2001
This is not the most recent version of the article. View current version (26 MAR 2014)
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.