VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems

doi:10.1021/acs.jcim.5b00687

	VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems
	Wang, Chaojie 1; Zheng, Suqing 1; Tang, Qing 1; He, Jian 2; Du, Shiyu 3; Xu, Shaofang 1; Xu, Yong 4; Lin, Fu 1
刊名	JOURNAL OF CHEMICAL INFORMATION AND MODELING
	2016-04-01
卷号	56 期号:4 页码:811-818
ISSN号	1549-9596
DOI	10.1021/acs.jcim.5b00687
文献子类	Article
英文摘要	Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for Metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.
WOS关键词	DYNAMICS SIMULATIONS ; NDDO APPROXIMATIONS ; METALLOPROTEINS ; PROTEINS ; BINDING ; OPTIMIZATION ; AUTOMATION ; PERCEPTION ; CATIONS ; WATER
WOS研究方向	Pharmacology & Pharmacy ; Chemistry ; Computer Science
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000375021100018
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/170794]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者	Lin, Fu
作者单位	1.Wenzhou Med Univ, Sch Pharmaceut Sci, Wenzhou 325035, Peoples R China 2.Chinese Acad Sci, Dalian Inst Chem Phys, Ctr Translat Med, Dept Biotechnol, 457 Zhongshan Rd, Dalian 116023, Liaoning, Peoples R China 3.Chinese Acad Sci, Ningbo Inst Materials Technol & Engn, Engn Lab Specialty Fibers & Nucl Energy Materials, 519 Zhuangshi Ave, Ningbo 315201, Zhejiang, Peoples R China 4.Chinese Acad Sci, Guangzhou Inst Biomed & Hlth, Ctr Chem Biol, 190 Kaiyuan Ave,Guangzhou Sci Pk, Guangzhou 510530, Guangdong, Peoples R China
推荐引用方式 GB/T 7714	Wang, Chaojie,Zheng, Suqing,Tang, Qing,et al. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2016,56(4):811-818.
APA	Wang, Chaojie.,Zheng, Suqing.,Tang, Qing.,He, Jian.,Du, Shiyu.,...&Lin, Fu.(2016).VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.JOURNAL OF CHEMICAL INFORMATION AND MODELING,56(4),811-818.
MLA	Wang, Chaojie,et al."VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems".JOURNAL OF CHEMICAL INFORMATION AND MODELING 56.4(2016):811-818.