Automatic atom type and bond type perception in molecular mechanical calculations
Automatic atom type and bond type perception in molecular mechanical calculations
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DOI：
10.1016/j.jmgm.2005.12.005
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发表时间：
2006-10-01
影响因子：
2.9
通讯作者：
Case, David A.
中科院分区：
文献类型：
--
作者：
Wang, Junmei;Wang, Wei;Case, David A.
在分子力学(MM)研究中，需要在能量计算之前确定分子的原子类型和/或键类型。我们提出了一种自动识别描述表中定义的原子类型的算法，以及一种仅基于原子连接性来分配键类型的自动算法。这些算法已经在琥珀包的一个新模块中实现。这个辅助模块，前厅(大致意思是“琥珀之前”)，可用于生成LEAP的必要输入-琥珀程序，以生成大多数有机分子的最小化、分子动力学等拓扑结构。这些操作背后的算法可能对其他分子机械组件以及需要指定原子类型和键类型的应用程序有用。(C)2005 Elsevier Inc.保留所有权利。
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.