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Related Experiment Videos

Development and testing of a general amber force field.

Junmei Wang1, Romain M Wolf, James W Caldwell

  • 1Encysive Pharmaceuticals Inc., 7000 Fannin, Houston, Texas 77030, USA.

Journal of Computational Chemistry
|April 30, 2004
PubMed
Summary

A new general Amber force field (GAFF) for organic molecules offers accurate molecular modeling. This computational chemistry tool is suitable for drug design and database searching.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Existing Amber force fields are limited to proteins and nucleic acids.
  • A need exists for a compatible force field for organic molecules in drug design.
  • Accurate molecular mechanics force fields are crucial for predicting molecular behavior.

Purpose of the Study:

  • To develop and validate a general Amber force field (GAFF) for organic molecules.
  • To ensure compatibility with existing Amber force fields for biomolecules.
  • To provide a tool for automated molecular modeling in drug discovery and database searching.

Main Methods:

  • GAFF was developed using empirical and heuristic models for force constants and partial atomic charges.
  • GAFF performance was evaluated by comparing minimized structures to crystallographic data (Test I).

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  • Gas phase minimizations of nucleic acid base pairs and conformational energy analyses were performed (Tests II and III).

    • Main Results:

    • GAFF showed a root-mean-square displacement of 0.26 A compared to crystallographic structures, comparable to Tripos 5.2.
    • For nucleic acid base pairs, GAFF achieved RMS displacements of 0.25 A and relative energies of 1.2 kcal/mol.
    • The RMS error for relative conformational energies was approximately 0.5 kcal/mol, demonstrating good accuracy.

    Conclusions:

    • GAFF is a versatile and accurate force field for a wide range of organic and pharmaceutical molecules.
    • Its compatibility with existing Amber force fields enhances its utility in biomolecular simulations.
    • GAFF's automated application makes it a valuable tool for rational drug design and large-scale database searching.