title: VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.
abstract: 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.
authors.affiliation: School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China.
authors.forename: Suqing
authors.initials: S
authors.lastname: Zheng
authors.affiliation: School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Tang
authors.affiliation: Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Shahekou, Dalian, Liaoning 116023, P. R. China.
authors.forename: Jian
authors.initials: J
authors.lastname: He
authors.affiliation: Engineering Laboratory of Specialty Fibers and Nuclear Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , 519 Zhuangshi Avenue, Zhenhai, Ningbo, Zhejiang 315201, P. R. China.
authors.forename: Shiyu
authors.initials: S
authors.lastname: Du
authors.affiliation: School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China.
authors.forename: Shaofang
authors.initials: S
authors.lastname: Xu
authors.affiliation: School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China.
authors.forename: Chaojie
authors.initials: C
authors.lastname: Wang
authors.affiliation: Center of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, P. R. China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xu
authors.affiliation: School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China.
authors.forename: Fu
authors.initials: F
authors.lastname: Lin
mesh_terms: D008670:Metals / Q000737:chemistry*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012984:Software
chemical_list: D008670:Metals