AmberTools

David A. Case; Hasan Metin Aktulga; Kellon Belfon; David S. Cerutti; G. Andrés Cisneros; Vinícius Wilian D. Cruzeiro; Negin Forouzesh; Timothy J. Giese; Andreas W. Götz; Holger Gohlke; Saeed Izadi; Koushik Kasavajhala; Mehmet C. Kaymak; Edward King; Tom Kurtzman; Tai Sung Lee; Pengfei Li; Jian Liu; Tyler Luchko; Ray Luo; Madushanka Manathunga; Matias R. Machado; Hai Minh Nguyen; Kurt A. O’Hearn; Alexey V. Onufriev; Feng Pan; Sergio Pantano; Ruxi Qi; Ali Rahnamoun; Ali Risheh; Stephan Schott-Verdugo; Akhil Shajan; Jason Swails; Junmei Wang; Haixin Wei; Xiongwu Wu; Yongxian Wu; Shi Zhang; Shiji Zhao; Qiang Zhu; Thomas E. Cheatham; Daniel R. Roe; Adrian Roitberg; Carlos Simmerling; Darrin M. York; Maria C. Nagan; Kenneth M. Merz

doi:10.1021/acs.jcim.3c01153

AmberTools

David A. Case
, Hasan Metin Aktulga
, Kellon Belfon
, David S. Cerutti
, G. Andrés Cisneros
, Vinícius Wilian D. Cruzeiro
, Negin Forouzesh
, Timothy J. Giese
, Andreas W. Götz
, Holger Gohlke
, Saeed Izadi
, Koushik Kasavajhala
, Mehmet C. Kaymak
, Edward King
, Tom Kurtzman
, Tai Sung Lee
, Pengfei Li
, Jian Liu
, Tyler Luchko
, Ray Luo

Madushanka Manathunga, Matias R. Machado, Hai Minh Nguyen, Kurt A. O’Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz

Rutgers - The State University of New Jersey, New Brunswick
Michigan State University
FOG Pharmaceuticals Inc.
Psivant Therapeutics
University of Texas at Dallas
Stanford University
California State University Los Angeles
University of California at San Diego
Heinrich Heine University Düsseldorf
Jülich Research Centre
Genentech, Inc
Stony Brook University
University of California at Irvine
City University of New York
Loyola University Chicago
Peking University
California State University Northridge
Institut Pasteur de Montevideo
Virginia Polytechnic Institute and State University
Florida State University
Southern University of Science and Technology
Entos, Inc.
University of Pittsburgh
National Institutes of Health
Nurix Therapeutics, Inc.
University of Utah
University of Florida

Research output: Contribution to journal › Article › peer-review

1671 Scopus citations

Abstract

AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

Original language	English
Pages (from-to)	6183-6191
Number of pages	9
Journal	Journal of Chemical Information and Modeling
Volume	63
Issue number	20
DOIs	https://doi.org/10.1021/acs.jcim.3c01153
State	Published - Oct 23 2023

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10.1021/acs.jcim.3c01153

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Case, D. A., Aktulga, H. M., Belfon, K., Cerutti, D. S., Cisneros, G. A., Cruzeiro, V. W. D., Forouzesh, N., Giese, T. J., Götz, A. W., Gohlke, H., Izadi, S., Kasavajhala, K., Kaymak, M. C., King, E., Kurtzman, T., Lee, T. S., Li, P., Liu, J., Luchko, T., ... Merz, K. M. (2023). AmberTools. Journal of Chemical Information and Modeling, 63(20), 6183-6191. https://doi.org/10.1021/acs.jcim.3c01153

@article{d71531b448f24f9d967b29afcd6675ef,

title = "AmberTools",

abstract = "AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.",

author = "Case, \{David A.\} and Aktulga, \{Hasan Metin\} and Kellon Belfon and Cerutti, \{David S.\} and Cisneros, \{G. Andr{\'e}s\} and Cruzeiro, \{Vin{\'i}cius Wilian D.\} and Negin Forouzesh and Giese, \{Timothy J.\} and G{\"o}tz, \{Andreas W.\} and Holger Gohlke and Saeed Izadi and Koushik Kasavajhala and Kaymak, \{Mehmet C.\} and Edward King and Tom Kurtzman and Lee, \{Tai Sung\} and Pengfei Li and Jian Liu and Tyler Luchko and Ray Luo and Madushanka Manathunga and Machado, \{Matias R.\} and Nguyen, \{Hai Minh\} and O{\textquoteright}Hearn, \{Kurt A.\} and Onufriev, \{Alexey V.\} and Feng Pan and Sergio Pantano and Ruxi Qi and Ali Rahnamoun and Ali Risheh and Stephan Schott-Verdugo and Akhil Shajan and Jason Swails and Junmei Wang and Haixin Wei and Xiongwu Wu and Yongxian Wu and Shi Zhang and Shiji Zhao and Qiang Zhu and Cheatham, \{Thomas E.\} and Roe, \{Daniel R.\} and Adrian Roitberg and Carlos Simmerling and York, \{Darrin M.\} and Nagan, \{Maria C.\} and Merz, \{Kenneth M.\}",

note = "Publisher Copyright: {\textcopyright} 2023 The Authors. Published by American Chemical Society.",

year = "2023",

month = oct,

day = "23",

doi = "10.1021/acs.jcim.3c01153",

language = "English",

volume = "63",

pages = "6183--6191",

journal = "Journal of Chemical Information and Modeling",

issn = "1549-9596",

number = "20",

}

Case, DA, Aktulga, HM, Belfon, K, Cerutti, DS, Cisneros, GA, Cruzeiro, VWD, Forouzesh, N, Giese, TJ, Götz, AW, Gohlke, H, Izadi, S, Kasavajhala, K, Kaymak, MC, King, E, Kurtzman, T, Lee, TS, Li, P, Liu, J, Luchko, T, Luo, R, Manathunga, M, Machado, MR, Nguyen, HM, O’Hearn, KA, Onufriev, AV, Pan, F, Pantano, S, Qi, R, Rahnamoun, A, Risheh, A, Schott-Verdugo, S, Shajan, A, Swails, J, Wang, J, Wei, H, Wu, X, Wu, Y, Zhang, S, Zhao, S, Zhu, Q, Cheatham, TE, Roe, DR, Roitberg, A, Simmerling, C, York, DM, Nagan, MC & Merz, KM 2023, 'AmberTools', Journal of Chemical Information and Modeling, vol. 63, no. 20, pp. 6183-6191. https://doi.org/10.1021/acs.jcim.3c01153

TY - JOUR

T1 - AmberTools

AU - Case, David A.

AU - Aktulga, Hasan Metin

AU - Belfon, Kellon

AU - Cerutti, David S.

AU - Cisneros, G. Andrés

AU - Cruzeiro, Vinícius Wilian D.

AU - Forouzesh, Negin

AU - Giese, Timothy J.

AU - Götz, Andreas W.

AU - Gohlke, Holger

AU - Izadi, Saeed

AU - Kasavajhala, Koushik

AU - Kaymak, Mehmet C.

AU - King, Edward

AU - Kurtzman, Tom

AU - Lee, Tai Sung

AU - Li, Pengfei

AU - Liu, Jian

AU - Luchko, Tyler

AU - Luo, Ray

AU - Manathunga, Madushanka

AU - Machado, Matias R.

AU - Nguyen, Hai Minh

AU - O’Hearn, Kurt A.

AU - Onufriev, Alexey V.

AU - Pan, Feng

AU - Pantano, Sergio

AU - Qi, Ruxi

AU - Rahnamoun, Ali

AU - Risheh, Ali

AU - Schott-Verdugo, Stephan

AU - Shajan, Akhil

AU - Swails, Jason

AU - Wang, Junmei

AU - Wei, Haixin

AU - Wu, Xiongwu

AU - Wu, Yongxian

AU - Zhang, Shi

AU - Zhao, Shiji

AU - Zhu, Qiang

AU - Cheatham, Thomas E.

AU - Roe, Daniel R.

AU - Roitberg, Adrian

AU - Simmerling, Carlos

AU - York, Darrin M.

AU - Nagan, Maria C.

AU - Merz, Kenneth M.

PY - 2023/10/23

Y1 - 2023/10/23

N2 - AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

AB - AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

UR - https://www.scopus.com/pages/publications/85175271512

U2 - 10.1021/acs.jcim.3c01153

DO - 10.1021/acs.jcim.3c01153

M3 - Article

C2 - 37805934

AN - SCOPUS:85175271512

SN - 1549-9596

VL - 63

SP - 6183

EP - 6191

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

IS - 20

ER -

AmberTools

Abstract

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