pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules

The construction of a molecular topology lile is a prerequisite for any classical molecular dynamics simulation. However, the generation of such a lile may he very challenging at times, especially for large supramolecules. While many tools are available to provide topologies for large proteins and other biomolecules, the scientific community researching nonbiological systems is not equally well equipped. Here, we present a practical tool to generate topologies for arbitrary supramolecules: The pyPolyBuilder. In addition to linear polymer chains, it also provides the possibility to generate topologies of arbitrary, large, branched molecules, such as, e.g., dendrimers. Furthermore, it also generates reasonable starting structures for simulations of these molecules. pyPolyBuilder is a standalone command-line tool implemented in python. Therefore, it may be easily incorporated in persisting simulation pipelines on any operating systems and with different simulation engines. pyPolyBuilder is freely available on github: https://github.com/mssm-labmmol/pypolybuilder

Automated summary

pyPolyBuilder is a practical tool implemented in Python for generating topologies of arbitrary supramolecules, suitable for linear polymer chains and large branched molecules, providing reasonable starting structures for simulations of these molecules. It can be easily incorporated into existing simulation pipelines on any operating system.