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The massively parallel computation of absolute binding free energy with awell-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida,M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S.Pande, J. Chem. Phys. ${\bf 123}$, 084108 (2005)]. As an application, weperform the binding affinity calculations of six theophylline-related ligandswith RNA aptamer. Basically, our method is applicable when using many computenodes to accelerate simulations, thus a parallel computing system is alsodeveloped. To further reduce the computational cost, the adequate non-uniformintervals of coupling constant $\lambda$, connecting two equilibrium states,namely bound and unbound, are determined. The absolute binding energies $\DeltaG$ thus obtained have effective linear relation between the computed andexperimental values. If the results of two other different methods arecompared, thermodynamic integration (TI) and molecular mechanicsPoisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda $et al$ [H.Gouda, I. D. Kuntz, D. A. Case, and P. A. Kollman, Biopolymers ${\bf 68}$, 16(2003)], the predictive accuracy of the relative values $\Delta\Delta G$ isalmost comparable to that of TI: the correlation coefficients (R) obtained are0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energiesmeanwhile, a constant energy shift of $\sim$ -7 kcal/mol against theexperimental values is evident. To solve this problem, several presumablereasons are investigated.

Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values