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For: Loferer MJ, Loeffler HH, Liedl KR. A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems. J Comput Chem 2003;24:1240-9. [PMID: 12820132 DOI: 10.1002/jcc.10283] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024;161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024]  Open
2
Barnes TA, Ellis S, Chen J, Plimpton SJ, Nash JA. Plugin-based interoperability and ecosystem management for the MolSSI Driver Interface Project. J Chem Phys 2024;160:214114. [PMID: 38832733 DOI: 10.1063/5.0214279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]  Open
3
Das S, Shimshi M, Raz K, Nitoker Eliaz N, Mhashal AR, Ansbacher T, Major DT. EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes. J Chem Theory Comput 2019;15:5116-5134. [DOI: 10.1021/acs.jctc.9b00366] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
4
Barnard AS. Challenges in modelling nanoparticles for drug delivery. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016;28:023002. [PMID: 26682622 DOI: 10.1088/0953-8984/28/2/023002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
5
Laino T, Mohamed F, Laio A, Parrinello M. An Efficient Real Space Multigrid QM/MM Electrostatic Coupling. J Chem Theory Comput 2015;1:1176-84. [PMID: 26631661 DOI: 10.1021/ct050123f] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
6
Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. J Comput Chem 2015;36:2064-74. [PMID: 26311531 PMCID: PMC4575649 DOI: 10.1002/jcc.24045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 01/06/2023]
7
Götz AW, Clark MA, Walker RC. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem 2014;35:95-108. [PMID: 24122798 PMCID: PMC4063945 DOI: 10.1002/jcc.23444] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 08/05/2013] [Accepted: 08/31/2013] [Indexed: 11/09/2022]
8
Meier K, Schmid N, van Gunsteren WF. Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages. J Comput Chem 2012;33:2108-17. [DOI: 10.1002/jcc.23047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 01/07/2023]
9
Okamoto T, Yamada K, Koyano Y, Asada T, Koga N, Nagaoka M. A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation. J Comput Chem 2010;32:932-42. [DOI: 10.1002/jcc.21678] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/12/2010] [Accepted: 08/18/2010] [Indexed: 11/10/2022]
10
An efficient implementation of a QM–MM method in SIESTA. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0816-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
11
Mata RA. Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes. Phys Chem Chem Phys 2010;12:5041-52. [DOI: 10.1039/b918608e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
12
Li H, Li W, Li S, Ma J. Fragmentation-Based QM/MM Simulations: Length Dependence of Chain Dynamics and Hydrogen Bonding of Polyethylene Oxide and Polyethylene in Aqueous Solutions. J Phys Chem B 2008;112:7061-70. [DOI: 10.1021/jp800777e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
13
Lin H, Truhlar DG. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. J Phys Chem A 2007;109:3991-4004. [PMID: 16833721 DOI: 10.1021/jp0446332] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
14
Woodcock HL, Hodošček M, Gilbert ATB, Gill PMW, Schaefer HF, Brooks BR. Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J Comput Chem 2007;28:1485-1502. [PMID: 17334987 DOI: 10.1002/jcc.20587] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
15
Woodcock HL, Hodoscek M, Brooks BR. Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms. J Phys Chem A 2007;111:5720-8. [PMID: 17555303 DOI: 10.1021/jp0714217] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
16
Zhang Y, Lin H, Truhlar DG. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. J Chem Theory Comput 2007;3:1378-98. [DOI: 10.1021/ct7000107] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Shao Y, Kong J. YinYang Atom:  A Simple Combined ab Initio Quantum Mechanical Molecular Mechanical Model. J Phys Chem A 2007;111:3661-71. [PMID: 17429951 DOI: 10.1021/jp067307q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Lin H, Truhlar DG. QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0143-z] [Citation(s) in RCA: 933] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
19
Melo A, Alfaia AJI, Reis JCR, Calado ART. Unusual Solvent Effect on a SN2 Reaction. A Quantum-Mechanical and Kinetic Study of the Menshutkin Reaction between 2-Amino-1-methylbenzimidazole and Iodomethane in the Gas Phase and in Acetonitrile. J Phys Chem B 2006;110:1877-88. [PMID: 16471759 DOI: 10.1021/jp055660a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Gresh N, Piquemal JP, Krauss M. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem 2005;26:1113-30. [PMID: 15934064 DOI: 10.1002/jcc.20244] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
21
Friesner RA, Guallar V. AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS. Annu Rev Phys Chem 2005;56:389-427. [PMID: 15796706 DOI: 10.1146/annurev.physchem.55.091602.094410] [Citation(s) in RCA: 445] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
22
Friesner RA. Combined quantum and molecular mechanics (QM/MM). DRUG DISCOVERY TODAY. TECHNOLOGIES 2004;1:253-260. [PMID: 24981493 DOI: 10.1016/j.ddtec.2004.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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