Automatic atom type and bond type perception in molecular mechanical calculations.

Automatic atom type and bond type perception in molecular mechanical calculations. Research Abstract Details 

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Automatic atom type and bond type perception in molecular mechanical calculations. Abstract Text:

Junmei Wang,Wei Wang,Peter A Kollman,David A Case,

In molecular mechanics (MM) studies, atom types and/or bond types of molecules are needed to determine prior to energy calculations. We present here an automatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity. The algorithms have been implemented in a new module of the AMBER packages. This auxiliary module, antechamber (roughly meaning "before AMBER"), can be applied to generate necessary inputs of leap-the AMBER program to generate topologies for minimization, molecular dynamics, etc., for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types.

Automatic atom type and bond type perception in molecular mechanical calculations. Publishing Authors By Initials

J Wang,W Wang,PA Kollman,DA Case,

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Automatic atom type and bond type perception in molecular mechanical calculations. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Journal of molecular graphics & modelling

VOLUME: 25

Page Numbers: 247-60

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ISSN: 1093-3263

DAY: 3

MONTH: 02

YEAR: 2006

Automatic atom type and bond type perception in molecular mechanical calculations. Information

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LANGUAGE: eng

NlmUniqueID: 9716237

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Grant and Affiliation Information for Automatic atom type and bond type perception in molecular mechanical calculations.

AFFILIATION: College of Chemistry, Peking University, Beijing 100871, China. jwang@encysive.com

Country: United States

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MEDLINETA: J Mol Graph Model

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