Main Objective | To ease the handling and loading of large polymers from monomer information | ||||||
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Key Outcomes |
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Completion Date |
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Problem Statement
Current polymer forcefields are generally limited in use to commonly encountered polymers. While very accurate, these forcefields are generally inflexible and cannot be used on novel polymers without retraining. In contrast, the OpenForceField Toolkit allows for the parameterization and simulation of almost all small molecules that may construct a polymer. Using the existing small molecule forcefields to estimate the parameters and charges of repeating subunits in a larger polymer would allow for faster simulation of novel systems.
Scope
This Project only focuses on the very start of adapting the OpenForceField Toolkit to simulate polymers, first developing and testing software infrastructure that can later be used in a scientific study. Namely, we will develop a workflow to load and/or create arbitrary polymers from a minimum amount of information about monomer chemical info and residue connectivity. Any scientific discussion of parameter or charge assignment is out of scope.
Milestones/Objectives
Completed | Description |
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Loading of Polymers from PDB using Manually Generated Substructures/workflow for manual generation of substructures | |
Generating substructures for homopolymers with 1) chemical information provided by a monomer smarts 2) polymer geometry provided by a PDB | |
Generating substructures for homopolymers with 1) chemical information provided by a monomer smarts 2) polymer geometry provided a connectivity mapping (such as a dictionary) | |
Generating substructures for heteropolymers with 1) chemical information provided by a monomer smarts 2) polymer geometry provided by a PDB | |
Generating substructures for heteropolymers with 1) chemical information provided by a monomer smarts 2) polymer geometry provided a connectivity mapping (such as a dictionary) | |