Automatic atom type and bond type perception in molecular mechanical   calculations

doi:10.1016/j.jmgm.2005.12.005

CORC > 北京大学 > 化学与分子工程学院

	Automatic atom type and bond type perception in molecular mechanical calculations
	Wang, Junmei ; Wang, Wei ; Kollman, Peter A. ; Case, David A.
刊名	分子图示法与模型杂志
	2006
关键词	atom type perception bond type perception antechamber residue topology force field parameters general AMBER force field (GAFF) FORCE-FIELD CONFORMATIONAL ENERGIES EFFICIENT GENERATION RESP METHODOLOGY AM1-BCC MODEL NUCLEIC-ACIDS PARAMETERIZATION MMFF94 VALIDATION GEOMETRIES
DOI	10.1016/j.jmgm.2005.12.005
英文摘要	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. (c) 2005 Elsevier Inc. All rights reserved.; Biochemical Research Methods; Biochemistry & Molecular Biology; Computer Science, Interdisciplinary Applications; Crystallography; Mathematical & Computational Biology; SCI(E); EI; PubMed; 762; ARTICLE; 2; 247-260; 25
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/199361]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Wang, Junmei,Wang, Wei,Kollman, Peter A.,et al. Automatic atom type and bond type perception in molecular mechanical calculations[J]. 分子图示法与模型杂志,2006.
APA	Wang, Junmei,Wang, Wei,Kollman, Peter A.,&Case, David A..(2006).Automatic atom type and bond type perception in molecular mechanical calculations.分子图示法与模型杂志.
MLA	Wang, Junmei,et al."Automatic atom type and bond type perception in molecular mechanical calculations".分子图示法与模型杂志 (2006).