Molecular mechanics simulation methods are commonly used to describe molecular properties of chemical systems. The accuracy of these methods depends on the quality of the parameters used in the model. In this presentation we will describe the ongoing project: ParamChem that is capable of automating the force field parameterization process. This cyberinfrastructure is featured with a user driven workflow which incorporates the parameter initialization, optimization and validation steps to achieve an optimized set of parameters (bond lengths and angles, dihedral angles and partial charges) used in the additive forcefield models. It leverages the existing GridChem cyberinfrastructure in production to support front-end user-interactivity like exploring data and managing jobs as well as middleware to handle communications between different layers of the cyberinfrastructure described below. In the front-layer, it adds a JAVA GUI interface called ParamCAD to generate parameterization related inputs. In the back-end, the OGCE(Open Grid Computing Environments) workflow suites are utilized to wrap the command line scripts that drive the executions of Gaussian and CHARMM packages into web services as building blocks of the workflow (with the GFAC tools) and compose the scientific workflow (with the Xbaya tools). The OGCE tools then use Globus tools like GridFTP for file management and GRAM for job management within the high performance computing  computing resources. We will show the practical examples of automatic parameterization processes for small drug-like molecules such as pyrrolidine or 3-Phenoxymethylpyrrolidine in the context of the CHARMM General Forcefield (CGenFF) with the Paramchem workflow using Xsede distributed  computing resources supported by National Science Foundation.

ParamChem: Cyberinfrastructure toward automated parametrization of  forcefields

243rd National Meeting (2012)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.