Parameterization of General Organic Polymers within the Open Force Field Framework.

ABSTRACT: Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems wi

SUBMITTER: Davel CM 

PROVIDER: S-EPMC11090695 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature