A three-point method for evaluations of AMBER force field parameters: An application to copper-based artificial nucleases

Yanyan Zhu, Yan Wang, Guangju Chen, Chang Guo Zhan

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


We present the theoretical evaluation of new AMBER force field parameters for 12 copper-based nucleases with bis(2-pyridylmethyl) amine, 2,2′-dipyridylamine, imidazole, N,N-bis(2-benzimidazolylmethyl) amine and their derivative ligands based on first-principles electronic structure calculations at the B3LYP level of theory. A three-point approach was developed to accurately and efficiently evaluate the force field parameters for the copper-based nucleases with the ligands. The protocol of RESP atomic charges has been used to calculate the atomic charge distributions of the studied copper-based nucleases. The evaluated force field parameters and RESP atomic charges have been successfully applied in the testing molecular mechanics calculations and molecular dynamics simulations on the nucleases and the nuclease-DNA complexes, respectively. It has been demonstrated that the developed force field parameters and atomic charges can consistently reproduce molecular geometries and conformations in the available X-ray crystal structures and can reasonably predict the interaction properties of the nucleases with DNA. The developed force field parameters in this work provide an extension of the AMBER force field for its application to computational modeling and simulations of the copper-based artificial nucleases associated with DNA.

Original languageEnglish
Pages (from-to)167-178
Number of pages12
JournalTheoretical Chemistry Accounts
Issue number3-4
StatePublished - Mar 2009

Bibliographical note

Funding Information:
Financial support from the National Natural Science Foundation of China (Nos. 20673011, 20631020 and 20771017) and the Major State Basic Research Development Programs (Grant No. G2004CB719900) is gratefully acknowledged. We also thank computing resources provided by the HPSC of Beijing Normal University.


  • AMBER force field parameter
  • Artificial metallonuclease
  • Copper complex
  • Three-point method

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry


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