NDLI: Rapid parameterization of small molecules using the Force Field Toolkit

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Rapid parameterization of small molecules using the Force Field Toolkit

Content Provider	PubMed Central
Author	Mayne, Christopher G. Saam, Jan Schulten, Klaus Emad, Tajkhorshid Gumbart, James C.
Abstract	The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics (MD) simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, e.g., GAFF and CGenFF, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, set up multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment).
Related Links	http://dx.doi.org/10.1002/jcc.23422
File Format	PDF
ISSN	01928651
e-ISSN	1096987X
Journal	Journal of computational chemistry
Issue Number	32
Volume Number	34
Language	English
Publisher Date	2013-12-15
Access Restriction	Open
Subject Keyword	Chemistry(all) Computational Mathematics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Chemistry Computational Mathematics

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