Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.

ABSTRACT: Incorporating pH into molecular dynamics simulations is vital for accurately capturing the fully coupled conformational, energetic, and protonation landscape of many systems. The constant-pH molecular dynamics (CpHMD) methodologies represent state-of-the-art approaches to achieve this, with stochastic titration CpHMD (st-CpHMD) currently being one of the most well-developed and validated methods. St-CpHMD is already compatible with both the GROMOS 54A7 and CHARMM 36m force fields, and we extend it here to support the AMBER 14SB force field available in the GROMACS software package. We introduce and validate a minor modification to the official atomic partial charges of ff14SB (to achieve neutralization of the main chain) to render them compatible with st-CpHMD, and we benchmark the final i

SUBMITTER: Sequeira JGN 

PROVIDER: S-EPMC12818765 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature