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Automation of AMOEBA polarizable force field parameterization for small molecules
Johnny C Wu1, Gaurav Chattree, Pengyu Ren
1Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA.
Theoretical Chemistry Accounts
|April 17, 2012
Summary
A new automated tool, Poltype, generates force field parameters for organic molecules. This method accurately predicts molecular properties and hydration free energies, aiding drug discovery.
Area of Science:
- Computational Chemistry
- Molecular Modeling
- Drug Discovery
Background:
- Accurate molecular modeling requires precise force field parameters.
- Generating these parameters for organic molecules is complex and time-consuming.
- Polarizable force fields, like AMOEBA, offer improved accuracy but need robust parameterization methods.
Purpose of the Study:
- To establish a protocol for generating AMOEBA polarizable force field parameters for small organic molecules.
- To implement an automated utility, Poltype, for this parameter generation process.
- To validate the accuracy and applicability of the generated parameters.
Main Methods:
- Developed a protocol and implemented the Poltype utility for automated parameter generation.
- Validated parameters against quantum mechanical calculations (dipole moments, geometry, electrostatic potential, conformational energy).
- Assessed performance in liquid-phase simulations, including hydration free energy calculations for neutral and charged molecules.
Main Results:
- Poltype successfully automates the generation of AMOEBA parameters for organic molecules.
- Parameters show good agreement with quantum mechanical calculations.
- Hydration free energy predictions exhibit low RMS error (<1 kcal/mol for neutral molecules) and high correlation (R=0.95, <3% error for salts).
Conclusions:
- The Poltype utility provides a satisfactory and convenient method for generating polarizable force field parameters.
- The validated parameters are suitable for applications in molecular simulations and drug discovery.
- Further improvements can be made through expanded studies on diverse organic and ionic molecules.
