Hydration free energy calculation of amino acid analogs by molecular dynamics.

Abstract

The paper deals with molecular dynamics calculation of solvation fi-ee energy of some amino acid side chain analogs in water by GROMACS sofh\'are and following Dillgroup calculation procedure. We calculated the fi-ee energy for turning off the Lennard-Jones interactions of 8 amino acid analogs including methane/Ala, n-hutan/Ile, isohutan/Leu, propane/Val, acetamid/Asn, p-cresol/Tyr, etanol/Thr and metanollSer represented with the OP ES-AA force field in TIP3P water models. We achieved a high degree of statistical precision in molecular dynamic simulations and by thermodynamic intergration method obtained the deviation of calculated fi'ee energy of hydration of about 0.02 - 0.60 kcal/mol fi'om the experimental hydration fiee energy measurements of the same molecules.