Automation of AMOEBA polarizable force field parameterization for small molecules |
| |
Authors: | Johnny?C?Wu Gaurav?Chattree Email author" target="_blank">Pengyu?RenEmail author |
| |
Institution: | (1) Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; |
| |
Abstract: | A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established,
and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation,
we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential,
and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of
a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase
simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental
values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted
HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype
is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved
by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter
database. |
| |
Keywords: | |
本文献已被 PubMed SpringerLink 等数据库收录! |
|