ACPYPE - AnteChamber PYthon Parser interfacE.
ACPYPE - AnteChamber PYthon Parser interfacE.
复制标题
DOI：
10.1186/1756-0500-5-367
复制
发表时间：
2012-07-23
影响因子：
1.8
通讯作者：
Vranken WF
中科院分区：
文献类型：
--
作者：
Sousa da Silva AW;Vranken WF
ACPYPE（或AnteChamber PYthon解析器接口）是围绕AnteChamber软件的包装脚本，它简化了小分子拓扑和各种分子动力学程序（如GROMACS， CHARMM和CNS）参数的生成。它是用Python编程语言编写的，作为与其他基于Python的应用程序(如CCPN软件套件（用于核磁共振数据分析）和ARIA（用于核磁共振数据的结构计算）接口的工具而开发的。ACPYPE是在GNU GPL v3下的开源代码，可以在http://www.ccpn.ac.uk/acpype上作为独立应用程序获得，也可以在http://webapps.ccpn.ac.uk/acpype上作为门户网站应用程序获得。我们通过三种方式验证了ACPYPE生成的拓扑结构：通过与标准氨基酸的默认AMBER拓扑结构进行比较；通过生成和验证PDB中大量配体的拓扑结构；并重新计算了PDB中5种蛋白质配体复合物的结构。ACPYPE是一种工具，可以简化不同分子力学程序中不同格式的拓扑和参数的自动生成，包括部分电荷的计算，同时面向对象，可与其他应用程序集成。
ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB. ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.