TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations

Polarizable force fields advance our understanding of electrostatic interactions in molecular systems; however, their widespread application is limited by the complexity of required molecular modeling. We here present TinkerModeller (TKM), a versatile software package designed to streamline the construction of biological systems in the Tinker molecular simulation software. The core functionality of TKM lies in its capacity to generate input files for complex molecular systems and facilitate the conversion from classical to polarizable force fields. With a user-friendly, standalone script, TKM provides an intuitive interface that supports users from molecular modeling through to postanalysis, creating a comprehensive platform for molecular dynamics simulations within Tinker. Furthermore, TKM includes an electric field (EF) postanalysis module, introducing a novel approach that employs charge methods and point charge approximations for efficient internal EF estimation. This module offers a computationally low-demand solution for high-throughput EF estimation. Our work paves the way for broader, more accessible use of polarizable force fields within Tinker and introduces a new method for EF estimation, advancing our capacity to explore electrostatic effects in biological and materials science applications.