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

Abstract

The construction of a molecular topology file is a prerequisite for any classical molecular dynamics simulation. However, the generation of such a file may be 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

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

“…These systems are typically generated in less than 5 min independent of the chain length and target force-field. This performance compares favorably to the recently published PyPolyBuilder, which takes about 8 min for a single chain of 1248 coordinates 29 . To further benchmark the performance of the structure generation, we also set up systems with 1 million residues, corresponding to 13 million coordinates for atomistic polystyrene.…”

“…The problem of generating parameter files is treated as a graph transformation within polyply. Graph transformations are commonly used in other tools for generation input parameters as well 19 , 29 . The graph transformation in polyply takes a residue graph and maps it into a higher resolution graph, which is agnostic to the target resolution.…”

“…Graph transformations are commonly used in other tools for generation input parameters as well. 19,29 The graph transformation in polyply takes a residue graph and maps it into a higher resolution graph, which is agnostic to the target resolution. A graph consists of nodes and edges.…”

“…Depending on the molecule or system there are a number of specific solutions. 20,[27][28][29][30] Some of those are in principle capable of generating parameters and coordinates. 29,30 However, available programs typically support only one force-field and are limited to specific (mostly linear) polymers implemented by the developers.…”

“…20,[27][28][29][30] Some of those are in principle capable of generating parameters and coordinates. 29,30 However, available programs typically support only one force-field and are limited to specific (mostly linear) polymers implemented by the developers. Website implementations 28,30 have the added problem that performance relies on server-load and it involves human-time having to interface with the website.…”