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Main Objective

To ease the handling and loading of large polymers from monomer information

Key Outcomes

  1. Successful automated loading of homopolymers and heteropolymers from monomer information

  2. Defining the extent of monomer information (chemical information, connectivity to adjacent residues, etc.) and how best to manipulate and input monomer information to load and create arbitrary polymers quickly

  3. Creation of arbitrary homo/heterpolymers from inputted user monomer information and residue connectivity

Completion Date

Status

IN PROGRESS

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

  •  

Loading of Polymers from PDB using Manually Generated Substructures/workflow for manual generation of substructures

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Generating substructures for homopolymers with 1) chemical information provided by a monomer smarts 2) polymer geometry provided by a PDB

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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)

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