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

Area of Science:

• Computational chemistry and molecular modeling.
• Biophysics and materials science.

Background:

• Polarizable force fields offer advanced insights into electrostatic interactions but are complex to implement.
• Existing molecular modeling workflows can be cumbersome, limiting the use of sophisticated force fields.

Purpose of the Study:

• To introduce TinkerModeller (TKM), a software package designed to streamline the construction and simulation of biological systems using Tinker.
• To facilitate the conversion between classical and polarizable force fields.
• To present a novel, computationally efficient module for electric field (EF) postanalysis.

Main Methods:

• Development of a user-friendly, standalone script (TKM) for generating input files for complex molecular systems.
• Implementation of a conversion utility for switching between classical and polarizable force fields.
• Integration of an electric field postanalysis module utilizing charge methods and point charge approximations.

Main Results:

• TKM provides an intuitive interface for molecular dynamics simulations within the Tinker software.
• The software successfully facilitates the setup of systems for polarizable force field simulations.
• The EF postanalysis module enables efficient, low-demand, high-throughput estimation of internal electric fields.

Conclusions:

• TinkerModeller significantly enhances the accessibility and ease of use of polarizable force fields in Tinker.
• The novel EF estimation module offers a valuable tool for analyzing electrostatic effects.
• This work promotes broader application of advanced simulation techniques in biological and materials science.