GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pK_a Predictions with Single-pH Simulations.

ABSTRACT: We present a GPU implementation of the continuous constant pH molecular dynamics (CpHMD) based on the most recent generalized Born implicit-solvent model in the pmemd engine of the Amber molecular dynamics package. To test the accuracy of the tool for rapid pK_a predictions, a series of 2 ns single-pH simulations were performed for over 120 titratable residues in 10 benchmark proteins that were previously used to test the various continuous CpHMD methods. The calculated pK_a's showed a root-mean-square deviation of 0.80 and correlation coefficient of 0.83 with respect to experiment. Also, 90% of the pK_a's were converged with estimated errors below 0.1 pH units. Surprisingly, this level of accuracy is similar to our previous replica

SUBMITTER: Harris RC 

PROVIDER: S-EPMC6934042 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature