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VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems
Zheng, Suqing1; Tang, Qing1; He, Jian2; Du, Shiyu3; Xu, Shaofang1; Wang, Chaojie1; Xu, Yong4; Lin, Fu1
Source PublicationJOURNAL OF CHEMICAL INFORMATION AND MODELING
2016-04-01
ISSN1549-9596
DOI10.1021/acs.jcim.5b00687
Volume56Issue:4Pages:811-818
Indexed BySCI
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine ; Physical Sciences ; Technology
WOS SubjectChemistry, Medicinal ; Chemistry, Multidisciplinary ; Computer Science, Information Systems ; Computer Science, Interdisciplinary Applications
WOS Research AreaPharmacology & Pharmacy ; Chemistry ; Computer Science
WOS KeywordDYNAMICS SIMULATIONS ; NDDO APPROXIMATIONS ; METALLOPROTEINS ; PROTEINS ; BINDING ; OPTIMIZATION ; AUTOMATION ; PERCEPTION ; CATIONS ; WATER
AbstractForce 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.
Language英语
WOS IDWOS:000375021100018
PublisherAMER CHEMICAL SOC
Citation statistics
Cited Times:19[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/170795
Collection中国科学院大连化学物理研究所
Corresponding AuthorLin, Fu
Affiliation1.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
Recommended Citation
GB/T 7714
Zheng, Suqing,Tang, Qing,He, Jian,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 Zheng, Suqing.,Tang, Qing.,He, Jian.,Du, Shiyu.,Xu, Shaofang.,...&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 Zheng, Suqing,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.
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