The availability of large, high-quality datasets is crucial for artificial intelligence design and discovery in chemistry. Despite the essential roles of solvents in chemistry, the rapid computational dataset generation of solution-phase molecular properties at the quantum mechanical level of theory was previously hampered by the complicated simulation procedure. Software toolkits that can automate the procedure to set up high-throughput explicit-solvent quantum chemistry (QC) calculations for arbitrary solutes and solvents in an open-source framework are still lacking. We developed AutoSolvate, an open-source toolkit, to streamline the workflow for QC calculation of explicitly solvated molecules. It automates the solvated-structure generation, force field fitting, configuration sampling, and the final extraction of microsolvated cluster structures that QC packages can readily use to predict molecular properties of interest. AutoSolvate is available through both a command line interface and a graphical user interface, making it accessible to the broader scientific community. To improve the quality of the initial structures generated by AutoSolvate, we investigated the dependence of solute–solvent closeness on solute/solvent identities and trained a machine learning model to predict the closeness and guide initial structure generation. Finally, we tested the capability of AutoSolvate for rapid dataset curation by calculating the outer-sphere reorganization energy of a large dataset of 166 redox couples, which demonstrated the promise of the AutoSolvate package for chemical discovery efforts.
REFERENCES
1.
M.
Rupp
, A.
Tkatchenko
, K. R.
Müller
, and O. A.
Von Lilienfeld
, “Fast and accurate modeling of molecular atomization energies with machine learning
,” Phys. Rev. Lett.
108
, 058301
(2012
).2.
L. C.
Blum
and J. L.
Reymond
, “970 million druglike small molecules for virtual screening in the chemical universe database GDB-13
,” J. Am. Chem. Soc.
131
, 8732
(2009
).3.
L.
Ruddigkeit
, R.
Van Deursen
, L. C.
Blum
, and J.-L.
Reymond
, “Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17
,” J. Chem. Inf. Model.
52
, 2864
(2012
).4.
R.
Ramakrishnan
, P. O.
Dral
, M.
Rupp
, and O. A.
Von Lilienfeld
, “Quantum chemistry structures and properties of 134 kilo molecules
,” Sci. Data
1
, 140022
(2014
).5.
D. G. A.
Smith
, A. T.
Lolinco
, Z. L.
Glick
, J.
Lee
, A.
Alenaizan
, T. A.
Barnes
, C. H.
Borca
, R.
Di Remigio
, D. L.
Dotson
, S.
Ehlert
, A. G.
Heide
, M. F.
Herbst
, J.
Hermann
, C. B.
Hicks
, J. T.
Horton
, A. G.
Hurtado
, P.
Kraus
, H.
Kruse
, S. J. R.
Lee
, J. P.
Misiewicz
, L. N.
Naden
, F.
Ramezanghorbani
, M.
Scheurer
, J. B.
Schriber
, A. C.
Simmonett
, J.
Steinmetzer
, J. R.
Wagner
, L.
Ward
, M.
Welborn
, D.
Altarawy
, J.
Anwar
, J. D.
Chodera
, A.
Dreuw
, H. J.
Kulik
, F.
Liu
, T. J.
Martínez
, D. A.
Matthews
, H. F.
Schaefer
, J.
Šponer
, J. M.
Turney
, L.-P.
Wang
, N.
De Silva
, R. A.
King
, J. F.
Stanton
, M. S.
Gordon
, T. L.
Windus
, C. D.
Sherrill
, and L. A.
Burns
, “Quantum chemistry common driver and databases (QCDB) and quantum chemistry engine (QCEngine): Automation and interoperability among computational chemistry programs
,” J. Chem. Phys.
155
, 204801
(2021
).6.
D. G. A.
Smith
, D.
Altarawy
, L. A.
Burns
, M.
Welborn
, L. N.
Naden
, L.
Ward
, S.
Ellis
, B. P.
Pritchard
, and T. D.
Crawford
, “The MolSSI QCArchive project: An open-source platform to compute, organize, and share quantum chemistry data
,” Wiley Interdiscip. Rev.: Comput. Mol. Sci.
11
, e1491
(2021
).7.
G.
Landrum
, RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling; accessed October 10, 2022.8.
M.
Lovrić
, J. M.
Molero
, and R.
Kern
, “PySpark and RDKit: Moving towards big data in cheminformatics
,” Mol. Inf.
38
, 1800082
(2019
).9.
E. I.
Ioannidis
, T. Z. H.
Gani
, and H. J.
Kulik
, “molSimplify: A toolkit for automating discovery in inorganic chemistry
,” J. Comput. Chem.
37
, 2106
(2016
).10.
S. P.
Ong
, W. D.
Richards
, A.
Jain
, G.
Hautier
, M.
Kocher
, S.
Cholia
, D.
Gunter
, V. L.
Chevrier
, K. A.
Persson
, and G.
Ceder
, “Python Materials Genomics (pymatgen): A robust, open-source Python library for materials analysis
,” Comput. Mater. Sci.
68
, 314
(2013
).11.
S. P.
Huber
, E.
Bosoni
, M.
Bercx
, J.
Bröder
, A.
Degomme
, V.
Dikan
, K.
Eimre
, E.
Flage-Larsen
, A.
Garcia
, L.
Genovese
, D.
Gresch
, C.
Johnston
, G.
Petretto
, S.
Poncé
, G.-M.
Rignanese
, C. J.
Sewell
, B.
Smit
, V.
Tseplyaev
, M.
Uhrin
, D.
Wortmann
, A. V.
Yakutovich
, A.
Zadoks
, P.
Zarabadi-Poor
, B.
Zhu
, N.
Marzari
, and G.
Pizzi
, “Common workflows for computing material properties using different quantum engines
,” npj Comput. Mater.
7
, 136
(2021
).12.
Y.
Guan
, V. M.
Ingman
, B. J.
Rooks
, and S. E.
Wheeler
, “AARON: An automated reaction optimizer for new catalysts
,” J. Chem. Theory Comput.
14
, 5249
(2018
).13.
V. M.
Ingman
, A. J.
Schaefer
, L. R.
Andreola
, and S. E.
Wheeler
, “QChASM: Quantum chemistry automation and structure manipulation
,” Wiley Interdiscip. Rev.: Comput. Mol. Sci.
11
, e1510
(2021
).14.
J.
Tomasi
and M.
Persico
, “Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
,” Chem. Rev.
94
, 2027
(1994
).15.
C. J.
Cramer
and D. G.
Truhlar
, “Implicit solvation models: Equilibria, structure, spectra, and dynamics
,” Chem. Rev.
99
, 2161
(1999
).16.
M.
Orozco
and F. J.
Luque
, “Theoretical methods for the description of the solvent effect in biomolecular systems
,” Chem. Rev.
100
, 4187
(2000
).17.
J.
Tomasi
, B.
Mennucci
, and R.
Cammi
, “Quantum mechanical continuum solvation models
,” Chem. Rev.
105
, 2999
(2005
).18.
S.
Miertuš
, E.
Scrocco
, and J.
Tomasi
, “Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects
,” Chem. Phys.
55
, 117
(1981
).19.
A.
Klamt
and G.
Schüürmann
, “COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
,” J. Chem. Soc., Perkin Trans. 2
1993
, 799
.20.
V.
Barone
and M.
Cossi
, “Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model
,” J. Phys. Chem. A
102
, 1995
(1998
).21.
T. N.
Truong
and E. V.
Stefanovich
, “A new method for incorporating solvent effect into the classical, ab initio molecular orbital and density functional theory frameworks for arbitrary shape cavity
,” Chem. Phys. Lett.
240
, 253
(1995
).22.
B.
Mennucci
, E.
Cancès
, and J.
Tomasi
, “Evaluation of solvent effects in isotropic and anisotropic dielectrics and in ionic solutions with a unified integral equation method: Theoretical bases, computational implementation, and numerical applications
,” J. Phys. Chem. B
101
, 10506
(1997
).23.
E.
Cancès
, B.
Mennucci
, and J.
Tomasi
, “A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
,” J. Chem. Phys.
107
, 3032
(1997
).24.
J.
Tomasi
, B.
Mennucci
, and E.
Cancès
, “The IEF version of the PCM solvation method: An overview of a new method addressed to study molecular solutes at the QM ab initio level
,” J. Mol. Struct.: THEOCHEM
464
, 211
(1999
).25.
J. L.
Pérez-Lustres
, F.
Rodriguez-Prieto
, M.
Mosquera
, T. A.
Senyushkina
, N. P.
Ernsting
, and S. A.
Kovalenko
, “Ultrafast proton transfer to solvent: Molecularity and intermediates from solvation- and diffusion-controlled regimes
,” J. Am. Chem. Soc.
129
, 5408
(2007
).26.
U.
Raucci
, M. G.
Chiariello
, and N.
Rega
, “Modeling excited-state proton transfer to solvent: A dynamics study of a super photoacid with a hybrid implicit/explicit solvent model
,” J. Chem. Theory Comput.
16
, 7033
(2020
).27.
J. M.
Boereboom
, P.
Fleurat-Lessard
, and R. E.
Bulo
, “Explicit solvation matters: Performance of QM/MM solvation models in nucleophilic addition
,” J. Chem. Theory Comput.
14
, 1841
(2018
).28.
M. M.
Pinney
, A.
Natarajan
, F.
Yabukarski
, D. M.
Sanchez
, F.
Liu
, R.
Liang
, T.
Doukov
, J. P.
Schwans
, T. J.
Martinez
, and D.
Herschlag
, “Structural coupling throughout the active site hydrogen bond networks of ketosteroid isomerase and photoactive yellow protein
,” J. Am. Chem. Soc.
140
, 9827
(2018
).29.
P. A.
Sigala
, E. A.
Ruben
, C. W.
Liu
, P. M. B.
Piccoli
, E. G.
Hohenstein
, T. J.
Martínez
, A. J.
Schultz
, and D.
Herschlag
, “Determination of hydrogen bond structure in water versus aprotic environments to test the relationship between length and stability
,” J. Am. Chem. Soc.
137
, 5730
(2015
).30.
A. W.
Götz
, M. A.
Clark
, and R. C.
Walker
, “An extensible interface for QM/MM molecular dynamics simulations with AMBER
,” J. Comput. Chem.
35
, 95
(2014
).31.
A.
Warshel
and M.
Levitt
, “Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
,” J. Mol. Biol.
103
, 227
(1976
).32.
U. C.
Singh
and P. A.
Kollman
, “A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers
,” J. Comput. Chem.
7
, 718
(1986
).33.
M. J.
Field
, P. A.
Bash
, and M.
Karplus
, “A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
,” J. Comput. Chem.
11
, 700
(1990
).34.
D.
Bakowies
and W.
Thiel
, “Hybrid models for combined quantum mechanical and molecular mechanical approaches
,” J. Phys. Chem.
100
, 10580
(1996
).35.
G. N.
Simm
, P. L.
Türtscher
, and M.
Reiher
, “Systematic microsolvation approach with a cluster-continuum scheme and conformational sampling
,” J. Comput. Chem.
41
, 1144
(2020
).36.
J.
Zhang
and M.
Dolg
, “ABCluster: The artificial bee colony algorithm for cluster global optimization
,” Phys. Chem. Chem. Phys.
17
, 24173
(2015
).37.
J.
Zhang
and M.
Dolg
, “Global optimization of clusters of rigid molecules using the artificial bee colony algorithm
,” Phys. Chem. Chem. Phys.
18
, 3003
(2016
).38.
E.
Hruska
, A.
Gale
, X.
Huang
, and F.
Liu
, AutoSolvate https://github.com/Liu-group/AutoSolvate; accessed October 01, 2022.39.
N. M.
O’Boyle
, M.
Banck
, C. A.
James
, C.
Morley
, T.
Vandermeersch
, and G. R.
Hutchison
, “Open Babel: An open chemical toolbox
,” J. Cheminf.
3
, 33
(2011
).40.
L.
Martínez
, R.
Andrade
, E. G.
Birgin
, and J. M.
Martínez
, “PACKMOL: A package for building initial configurations for molecular dynamics simulations
,” J. Comput. Chem.
30
, 2157
(2009
).41.
Anaconda Software Distribution https://docs.anaconda.com/; accessed October 01, 2022.
42.
O.
Ben-Kiki
, C.
Evans
, and B.
Ingerson
, YAML ain’t markup language (YAMLTM) version 1.1, Working Draft 2008-05 11 (2009).43.
J. E.
Grayson
, Python and Tkinter Programming
(Manning Publications Co.
, Greenwich
, 2000
).44.
J. W.
Shipman
, Tkinter 8.4 Reference: A GUI for Python
(New Mexico Tech Computer Center
, 2013
), Vol. 54.45.
B. B.
Welch
, K.
Jones
, and J.
Hobbs
, Practical Programming in Tcl/Tk
(Prentice Hall Professional
, 2003
).46.
J. L.
Sussman
, D.
Lin
, J.
Jiang
, N. O.
Manning
, J.
Prilusky
, O.
Ritter
, and E. E.
Abola
, “Protein data bank (PDB): Database of three-dimensional structural information of biological macromolecules
,” Acta Crystallogr., Sect. D: Struct. Biol.
54
, 1078
(1998
).47.
J. W.
Ponder
and D. A.
Case
, “Force fields for protein simulations
,” Adv. Protein Chem.
66
, 27
(2003
).48.
J.
Wang
, R. M.
Wolf
, J. W.
Caldwell
, P. A.
Kollman
, and D. A.
Case
, “Development and testing of a general amber force field
,” J. Comput. Chem.
25
, 1157
(2004
).49.
J.
Wang
, W.
Wang
, P. A.
Kollman
, and D. A.
Case
, “Automatic atom type and bond type perception in molecular mechanical calculations
,” J. Mol. Graphics Modell.
25
, 247
(2006
).50.
C. I.
Bayly
, P.
Cieplak
, W.
Cornell
, and P. A.
Kollman
, “A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
,” J. Phys. Chem.
97
, 10269
(1993
).51.
W. D.
Cornell
, P.
Cieplak
, C. I.
Bayly
, and P. A.
Kollman
, “Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
,” J. Am. Chem. Soc.
115
, 9620
(2002
).52.
M. J.
Frisch
, G. W.
Trucks
, H. B.
Schlegel
, G. E.
Scuseria
, M. A.
Robb
, J. R.
Cheeseman
, G.
Scalmani
, V.
Barone
, G. A.
Petersson
, H.
Nakatsuji
, X.
Li
, M.
Caricato
, A. V.
Marenich
, J.
Bloino
, B. G.
Janesko
, R.
Gomperts
, B.
Mennucci
, H. P.
Hratchian
, J. V.
Ortiz
, A. F.
Izmaylov
, J. L.
Sonnenberg
, D.
Williams-Young
, F.
Ding
, F.
Lipparini
, F.
Egidi
, J.
Goings
, B.
Peng
, A.
Petrone
, T.
Henderson
, D.
Ranasinghe
, V. G.
Zakrzewski
, J.
Gao
, N.
Rega
, G.
Zheng
, W.
Liang
, M.
Hada
, M.
Ehara
, K.
Toyota
, R.
Fukuda
, J.
Hasegawa
, M.
Ishida
, T.
Nakajima
, Y.
Honda
, O.
Kitao
, H.
Nakai
, T.
Vreven
, K.
Throssell
, J. A.
Montgomery
, Jr., J. E.
Peralta
, F.
Ogliaro
, M. J.
Bearpark
, J. J.
Heyd
, E. N.
Brothers
, K. N.
Kudin
, V. N.
Staroverov
, T. A.
Keith
, R.
Kobayashi
, J.
Normand
, K.
Raghavachari
, A. P.
Rendell
, J. C.
Burant
, S. S.
Iyengar
, J.
Tomasi
, M.
Cossi
, J. M.
Millam
, M.
Klene
, C.
Adamo
, R.
Cammi
, J. W.
Ochterski
, R. L.
Martin
, K.
Morokuma
, O.
Farkas
, J. B.
Foresman
, and D. J.
Fox
, Gaussian 16, Revision C.01; accessed October 01, 2022.53.
A.
Jakalian
, D. B.
Jack
, and C. I.
Bayly
, “Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
,” J. Comput. Chem.
23
, 1623
(2002
).54.
Tripos, Tripos Mol2 File Format, 1988.
55.
L.
Martínez
, R.
Andrade
, E. G.
Birgin
, and J. M.
Martínez
, “PACKMOL: A package for building initial configurations for molecular dynamics simulations
,” J. Comput. Chem.
30
, 2157
(2009
).56.
Bryce Group, Amber Parameter Database, http://amber.manchester.ac.uk/; accessed October 01, 2022.
57.
H.
Neugebauer
, F.
Bohle
, M.
Bursch
, A.
Hansen
, and S.
Grimme
, “Benchmark study of electrochemical redox potentials calculated with semi-empirical and DFT methods
,” J. Phys. Chem. A
124
, 7166
(2020
).58.
S.
Grimme
, S.
Ehrlich
, and L.
Goerigk
, “Effect of the damping function in dispersion corrected density functional theory
,” J. Comput. Chem.
32
, 1456
(2011
).59.
E.
Hruska
, A.
Gale
, and F.
Liu
, “Bridging the experiment-calculation divide: Machine learning corrections to redox potential calculations in implicit and explicit solvent models
,” J. Chem. Theory Comput.
18
, 1096
(2022
).60.
L.
Martínez
and S.
Shimizu
, “Molecular interpretation of preferential interactions in protein solvation: A solvent-shell perspective by means of minimum-distance distribution functions
,” J. Chem. Theory Comput.
13
, 6358
(2017
).61.
L.
Martínez
, “ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective
,” J. Mol. Liq.
347
, 117945
(2021
).62.
L.
Cai
, W.
Lv
, H.
Zhu
, and Q.
Xu
, “Molecular dynamics simulation on adsorption of pyrene-polyethylene onto ultrathin single-walled carbon nanotube
,” Physica E
81
, 226
(2016
).63.
H. F.
Jerome
, “Greedy function approximation: A gradient boosting machine
,” Ann. Stat.
29
, 1189
(2001
).64.
S.
De
, A. P.
Bartók
, G.
Csányi
, and M.
Ceriotti
, “Comparing molecules and solids across structural and alchemical space
,” Phys. Chem. Chem. Phys.
18
, 13754
(2016
).65.
L.
Himanen
, M. O. J.
Jäger
, E. V.
Morooka
, F.
Federici Canova
, Y. S.
Ranawat
, D. Z.
Gao
, P.
Rinke
, and A. S.
Foster
, “DScribe: Library of descriptors for machine learning in materials science
,” Comput. Phys. Commun.
247
, 106949
(2020
).66.
R. A.
Marcus
and N.
Sutin
, “Electron transfers in chemistry and biology
,” Biochim. Biophys. Acta, Rev. Bioenerg.
811
, 265
(1985
).67.
J.
Blumberger
, “Recent advances in the theory and molecular simulation of biological electron transfer reactions
,” Chem. Rev.
115
, 11191
(2015
).68.
J.
Blumberger
, “Free energies for biological electron transfer from QM/MM calculation: Method, application and critical assessment
,” Phys. Chem. Chem. Phys.
10
, 5651
(2008
).69.
B. S.
Brunschwig
and N.
Sutin
, “Energy surfaces, reorganization energies, and coupling elements in electron transfer
,” Coord. Chem. Rev.
187
, 233
(1999
).70.
V.
Vaissier
, P.
Barnes
, J.
Kirkpatrick
, and J.
Nelson
, “Influence of polar medium on the reorganization energy of charge transfer between dyes in a dye sensitized film
,” Phys. Chem. Chem. Phys.
15
, 4804
(2013
).71.
L.
Eberson
, R.
Gonzalez-Luque
, J.
Lorentzon
, M.
Merchan
, and B. O.
Roos
, “The ab initio calculation of inner sphere reorganization energies of inorganic redox couples
,” J. Am. Chem. Soc.
115
, 2898
(1993
).72.
E.
Falbo
and T. J.
Penfold
, “Redox potentials of polyoxometalates from an implicit solvent model and QM/MM molecular dynamics
,” J. Phys. Chem. C
124
, 15045
(2020
).73.
X.
Jiang
, Z.
Futera
, and J.
Blumberger
, “Ergodicity-breaking in thermal biological electron transfer? Cytochrome C revisited
,” J. Phys. Chem. B
123
, 7588
(2019
).74.
K. A.
Sharp
, “Calculation of electron transfer reorganization energies using the finite difference Poisson-Boltzmann model
,” Biophys. J.
74
, 1241
(1998
).75.
Y.-P.
Liu
and M. D.
Newton
, “Reorganization energy for electron transfer at film-modified electrode surfaces: A dielectric continuum model
,” J. Phys. Chem.
98
, 7162
(1994
).76.
S. U. M.
Khan
and J.
O’Mara Bockris
, “Contribution of inner-sphere reorganization in electron-transfer reaction in solution
,” Chem. Phys. Lett.
99
, 83
(1983
).77.
S. U. M.
Khan
and J. O.
Bockris
, “Relative contributions of inner- and outer-shell reorganization in electron-transfer reactions in solution
,” J. Phys. Chem.
87
, 4012
(1983
).78.
E.
Maggio
, N.
Martsinovich
, and A.
Troisi
, “Evaluating charge recombination rate in dye-sensitized solar cells from electronic structure calculations
,” J. Phys. Chem. C
116
, 7638
(2012
).79.
M.
Buda
, “On calculating reorganization energies for electrochemical reactions using density functional theory and continuum solvation models
,” Electrochim. Acta
113
, 536
(2013
).80.
G. M. J.
Barca
, C.
Bertoni
, L.
Carrington
, D.
Datta
, N.
De Silva
, J. E.
Deustua
, D. G.
Fedorov
, J. R.
Gour
, A. O.
Gunina
, E.
Guidez
, T.
Harville
, S.
Irle
, J.
Ivanic
, K.
Kowalski
, S. S.
Leang
, H.
Li
, W.
Li
, J. J.
Lutz
, I.
Magoulas
, J.
Mato
, V.
Mironov
, H.
Nakata
, B. Q.
Pham
, P.
Piecuch
, D.
Poole
, S. R.
Pruitt
, A. P.
Rendell
, L. B.
Roskop
, K.
Ruedenberg
, T.
Sattasathuchana
, M. W.
Schmidt
, J.
Shen
, L.
Slipchenko
, M.
Sosonkina
, V.
Sundriyal
, A.
Tiwari
, J. L.
Galvez Vallejo
, B.
Westheimer
, M.
Włoch
, P.
Xu
, F.
Zahariev
, and M. S.
Gordon
, “Recent developments in the general atomic and molecular electronic structure system
,” J. Phys. Chem.
152
, 154102
(2020
).81.
D. G. A.
Smith
, L. A.
Burns
, A. C.
Simmonett
, R. M.
Parrish
, M. C.
Schieber
, R.
Galvelis
, P.
Kraus
, H.
Kruse
, R.
Di Remigio
, A.
Alenaizan
, A. M.
James
, S.
Lehtola
, J. P.
Misiewicz
, M.
Scheurer
, R. A.
Shaw
, J. B.
Schriber
, Y.
Xie
, Z. L.
Glick
, D. A.
Sirianni
, J. S.
O’Brien
, J. M.
Waldrop
, A.
Kumar
, E. G.
Hohenstein
, B. P.
Pritchard
, B. R.
Brooks
, H. F.
Schaefer
, A. Y.
Sokolov
, K.
Patkowski
, A. E.
Deprince
, U.
Bozkaya
, R. A.
King
, F. A.
Evangelista
, J. M.
Turney
, T. D.
Crawford
, and C. D.
Sherrill
, “Psi4 1.4: Open-source software for high-throughput quantum chemistry
,” J. Chem. Phys.
152
, 184108
(2020
).82.
F.-Y.
Dupradeau
, A.
Pigache
, T.
Zaffran
, C.
Savineau
, R.
Lelong
, N.
Grivel
, D.
Lelong
, W.
Rosanski
, and P.
Cieplak
, “The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building
,” Phys. Chem. Chem. Phys.
12
, 7821
(2010
).83.
E.
Vanquelef
, S.
Simon
, G.
Marquant
, E.
Garcia
, G.
Klimerak
, J. C.
Delepine
, P.
Cieplak
, and F.-Y.
Dupradeau
, “R.E.D. server: A web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments
,” Nucleic Acids Res.
39
, W511
(2011
).84.
F.
Wang
, J.-P.
Becker
, P.
Cieplak
, and F.-Y.
Dupradeau
, in Abstracts of Papers of the American Chemical Society
(American Chemical Society
, 2014
).85.
P.
Eastman
, J.
Swails
, J. D.
Chodera
, R. T.
McGibbon
, Y.
Zhao
, K. A.
Beauchamp
, L.-P.
Wang
, A. C.
Simmonett
, M. P.
Harrigan
, C. D.
Stern
, R. P.
Wiewiora
, B. R.
Brooks
, and V. S.
Pande
, “OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
,” PLoS Comput. Biol.
13
, e1005659
(2017
).86.
B. R.
Brooks
, C. L.
Brooks
, A. D.
Mackerell
, L.
Nilsson
, R. J.
Petrella
, B.
Roux
, Y.
Won
, G.
Archontis
, C.
Bartels
, S.
Boresch
, A.
Caflisch
, L.
Caves
, Q.
Cui
, A. R.
Dinner
, M.
Feig
, S.
Fischer
, J.
Gao
, M.
Hodoscek
, W.
Im
, K.
Kuczera
, T.
Lazaridis
, J.
Ma
, V.
Ovchinnikov
, E.
Paci
, R. W.
Pastor
, C. B.
Post
, J. Z.
Pu
, M.
Schaefer
, B.
Tidor
, R. M.
Venable
, H. L.
Woodcock
, X.
Wu
, W.
Yang
, D. M.
York
, and M.
Karplus
, “CHARMM: The biomolecular simulation program
,” J. Comput. Chem.
30
, 1545
(2009
).87.
M. J.
Abraham
, T.
Murtola
, R.
Schulz
, S.
Páll
, J. C.
Smith
, B.
Hess
, and E.
Lindahl
, “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
,” SoftwareX
1–2
, 19
(2015
).88.
J.
Towns
, T.
Cockerill
, M.
Dahan
, I.
Foster
, K.
Gaither
, A.
Grimshaw
, V.
Hazlewood
, S.
Lathrop
, D.
Lifka
, G. D.
Peterson
, R.
Roskies
, J. R.
Scott
, and N.
Wilkins-Diehr
, “XSEDE: Accelerating scientific discovery
,” Comput. Sci. Eng.
16
, 62
(2014
).89.
D. A.
Case
, H. M.
Aktulga
, K.
Belfon
, I. Y.
Ben-Shalom
, S. R.
Brozell
, D. S.
Cerutti
, T. E.
Cheatham, III
, G. A.
Cisneros
, V. W. D.
Cruzeiro
, T. A.
Darden
, R. E.
Duke
, G.
Giambasu
, M. K.
Gilson
, H.
Gohlke
, A. W.
Goetz
, R.
Harris
, S.
Izadi
, S. A.
Izmailov
, C.
Jin
, K.
Kasavajhala
, M. C.
Kaymak
, E.
King
, A.
Kovalenko
, T.
Kurtzman
, T. S.
LEe
, S.
LeGrand
, P.
Li
, C.
Lin
, J.
Liu
, T.
Luchko
, R.
Luo
, M.
Machado
, V.
Man
, M.
Manathunga
, K. M.
Merz
, Y.
Miao
, O.
Mikhailovskii
, G.
Monard
, H.
Nguyen
, K. A.
O'Hearn
, A.
Onufriev
, F.
Pan
, S.
Pantano
, R.
Qi
, A.
Rahnamoun
, D. R.
Roe
, A.
Roitberg
, C.
Sagui
, S.
Schott-Verdugo
, J.
Shen
, C. L.
Simmerling
, N. R.
Skrynnikov
, J.
Smith
, J.
Swails
, R. C.
Walker
, J.
Wang
, H.
Wei
, R. M.
Wolf
, X.
Wu
, Y.
Xue
, D. M.
York
, S.
Zhao
, and P. A.
Kollman
, computer program Amber20, University of California, San Francisco, 2014
; available at https://ambermd.org/CiteAmber.php.© 2022 Author(s). Published under an exclusive license by AIP Publishing.
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