| MATCH: an atom-typing toolset for molecular mechanics force fields. | |
| | |
MedLine Citation:
|
PMID: 22042689 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized. |
| | |
Authors:
|
Joseph D Yesselman; Daniel J Price; Jennifer L Knight; Charles L Brooks |
Related Documents
:
|
20829959 - Teflon laps: some new developments and results. 21974419 - A semi-analytical ray method to predict the propagation of long-range vertical noise: a... 21973759 - Seismo-acoustic propagation effects at the seafloor with applications to geoacoustic in... 17782049 - Picosecond resolution in scanning tunneling microscopy. 20523659 - Compact optical head using a holographic optical element for cd players. 21893329 - Determination of acoustic impedances of multi matching layers for narrowband ultrasonic... 11864019 - Dissipative longitudinal solitons in a two-dimensional strongly coupled complex (dusty)... 1609829 - Hemifacial microsomia: developmental consequence of perturbation of the auriculofacial ... 19844309 - Liquid tunable double-focus lens fabricated with diamond cutting and soft lithography. |
Publication Detail:
|
Type: Journal Article; Research Support, N.I.H., Extramural Date: 2011-11-01 |
Journal Detail:
|
Title: Journal of computational chemistry Volume: 33 ISSN: 1096-987X ISO Abbreviation: J Comput Chem Publication Date: 2012 Jan |
Date Detail:
|
Created Date: 2011-12-01 Completed Date: 2012-07-12 Revised Date: 2013-05-23 |
Medline Journal Info:
|
Nlm Unique ID: 9878362 Medline TA: J Comput Chem Country: United States |
Other Details:
|
Languages: eng Pagination: 189-202 Citation Subset: IM |
Copyright Information:
|
Copyright © 2011 Wiley Periodicals, Inc. |
Affiliation:
|
Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, USA. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Algorithms Databases, Factual Quantum Theory* Software* |
| Grant Support | |
ID/Acronym/Agency:
|
GM037554/GM/NIGMS NIH HHS; R01 GM037554-24/GM/NIGMS NIH HHS; R01 GM037554-25/GM/NIGMS NIH HHS |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Paleodiet of Extinct Platyrrhines With Emphasis on the Caribbean Forms: Three-Dimensional Geometric ...
Next Document: Correlation between BIS and GCS in patients suffering from head injury.