AmberTools

David A Case¹, Hasan Metin Aktulga², Kellon Belfon³, David S Cerutti⁴, G Andrés Cisneros⁵, Vinícius Wilian D Cruzeiro⁶, Negin Forouzesh⁷, Timothy J Giese⁸, Andreas W Götz⁹, Holger Gohlke^{10

11}, Saeed Izadi¹², Koushik Kasavajhala¹³, Mehmet C Kaymak², Edward King¹⁴, Tom Kurtzman^{15

16}, Tai-Sung Lee⁸, Pengfei Li¹⁷, Jian Liu¹⁸, Tyler Luchko¹⁹, Ray Luo¹⁴, Madushanka Manathunga²⁰, Matias R Machado²¹, Hai Minh Nguyen¹, Kurt A O'Hearn², Alexey V Onufriev²², Feng Pan²³, Sergio Pantano²¹, Ruxi Qi²⁴, Ali Rahnamoun², Ali Risheh⁷, Stephan Schott-Verdugo¹¹, Akhil Shajan²⁰, Jason Swails²⁵, Junmei Wang²⁶, Haixin Wei¹⁴, Xiongwu Wu²⁷, Yongxian Wu¹⁴, Shi Zhang⁸, Shiji Zhao^{14

28}, Qiang Zhu¹⁴, Thomas E Cheatham 3rd²⁹, Daniel R Roe³⁰, Adrian Roitberg³¹, Carlos Simmerling¹³, Darrin M York⁸, Maria C Nagan³², Kenneth M Merz Jr²⁰

Affiliations

¹ Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
² Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.
³ FOG Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States.
⁴ Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States.
⁵ Department of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States.
⁶ Department of Chemistry and The PULSE Institute, Stanford University, Stanford 94305, California, United States.
⁷ Department of Computer Science, California State University, Los Angeles 90032, California, United States.
⁸ Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
⁹ San Diego Supercomputer Center, University of California San Diego, La Jolla 92093-0505, California, United States.
¹⁰ Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.
¹¹ Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
¹² Pharmaceutical Development, Genentech, Inc., South San Francisco 94080, California, United States.
¹³ Laufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.
¹⁴ Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.
¹⁵ Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States.
¹⁶ Department of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States.
¹⁷ Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago 60660, Illinois, United States.
¹⁸ Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
¹⁹ Department of Physics and Astronomy, California State University, Northridge, Northridge 91330, California, United States.
²⁰ Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.
²¹ Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
²² Departments of Computer Science and Physics, Virginia Tech, Blacksburg 24061, Virginia, United States.
²³ Department of Statistics, Florida State University, Tallahassee 32304, Florida, United States.
²⁴ Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China.
²⁵ Entos, 4470 W Sunset Blvd, Suite 107, Los Angeles 90027, California, United States.
²⁶ Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States.
²⁷ Laboratory of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States.
²⁸ Nurix Therapeutics, Inc., San Francisco 94158, California, United States.
²⁹ Department of Medicinal Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United States.
³⁰ Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States.
³¹ Department of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States.
³² Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.

PMID: 37805934
PMCID: PMC10598796
DOI: 10.1021/acs.jcim.3c01153

AmberTools

David A Case et al. J Chem Inf Model. 2023.

. 2023 Oct 23;63(20):6183-6191.

doi: 10.1021/acs.jcim.3c01153. Epub 2023 Oct 8.

Authors

Affiliations

¹ Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
² Department of Computer Science and Engineering, Michigan State University, East Lansing 48824-1322, Michigan, United States.
³ FOG Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States.
⁴ Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States.
⁵ Department of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States.
⁶ Department of Chemistry and The PULSE Institute, Stanford University, Stanford 94305, California, United States.
⁷ Department of Computer Science, California State University, Los Angeles 90032, California, United States.
⁸ Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.
⁹ San Diego Supercomputer Center, University of California San Diego, La Jolla 92093-0505, California, United States.
¹⁰ Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.
¹¹ Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
¹² Pharmaceutical Development, Genentech, Inc., South San Francisco 94080, California, United States.
¹³ Laufer Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.
¹⁴ Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States.
¹⁵ Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States.
¹⁶ Department of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States.
¹⁷ Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago 60660, Illinois, United States.
¹⁸ Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
¹⁹ Department of Physics and Astronomy, California State University, Northridge, Northridge 91330, California, United States.
²⁰ Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States.
²¹ Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
²² Departments of Computer Science and Physics, Virginia Tech, Blacksburg 24061, Virginia, United States.
²³ Department of Statistics, Florida State University, Tallahassee 32304, Florida, United States.
²⁴ Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China.
²⁵ Entos, 4470 W Sunset Blvd, Suite 107, Los Angeles 90027, California, United States.
²⁶ Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States.
²⁷ Laboratory of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States.
²⁸ Nurix Therapeutics, Inc., San Francisco 94158, California, United States.
²⁹ Department of Medicinal Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United States.
³⁰ Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States.
³¹ Department of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States.
³² Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States.

PMID: 37805934
PMCID: PMC10598796
DOI: 10.1021/acs.jcim.3c01153

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.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

**Figure 1**
Common workflow in AmberTools. Flow went from top to bottom. Black boxes are for preparation, gray indicates an optional preparation step specific for membrane systems, blue for simulation, and red for analysis.

**Figure 2**
**Overview of the Amber Tutorials.** Tutorials are modular, cover the basic steps of a typical molecular dynamics simulation, introductory case studies, advanced methods, and some tools that are commonly employed by Amber users.

See this image and copyright information in PMC

References

1. Weiner P. K.; Kollman P. A. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 1981, 2, 287–303. 10.1002/jcc.540020311. - DOI
1. Case D. A.; Cheatham T. E. 3rd; Darden T.; Gohlke H.; Luo R.; Merz K. M. Jr.; Onufriev A.; Simmerling C.; Wang B.; Woods R. J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668–1688. 10.1002/jcc.20290. - DOI - PMC - PubMed
1. Pearlman D.; Case D. A.; Caldwell J.; Ross W. S.; Cheatham T. E. II; DeBolt S.; Ferguson D.; Seibel G.; Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 1995, 91, 1–41. 10.1016/0010-4655(95)00041-D. - DOI
1. Salomon-Ferrer R.; Case D. A.; Walker R. C. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 2013, 3, 198–210. 10.1002/wcms.1121. - DOI
1. Ponder J. W.; Case D. A. Force fields for protein simulations. Adv. Protein Chem. 2003, 66, 27–85. 10.1016/S0065-3233(03)66002-X. - DOI - PubMed

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AmberTools

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Conflict of interest statement

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