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Amber 2022
Reference Manual
(Covers Amber22 and AmberTools22)
Amber 2022
Reference Manual
(Covers Amber22 and AmberTools22)
Principal contributors to the current codes:
David A. Case (Rutgers)
Ross C. Walker (UC San Diego, Agenus)
Thomas E. Cheatham III (Utah)
Carlos Simmerling (Stony Brook)
Adrian Roitberg (Florida)
Kenneth M. Merz (Michigan State)
Ray Luo (UC Irvine)
Pengfei Li (Loyola University Chicago)
Tom Darden (OpenEye)
Celeste Sagui (NCSU)
Feng Pan (FSU)
Junmei Wang (Pitt)
Daniel R. Roe (NIH)
Scott LeGrand (NVIDIA)
Jason Swails (Entos, Inc.)
Andreas W. Götz (UC San Diego)
Jamie Smith (NVIDIA)
David Cerutti (Roivant Discovery)
Taisung Lee (Rutgers)
Darrin York (Rutgers)
Tyler Luchko (CSU Northridge)
Viet Man (Pitt)
Vinícius Wilian D. Cruzeiro (Stanford)
Gérald Monard (U. Lorraine)
Yinglong Miao (Kansas)
Jinan Wang (Kansas)
Romain M. Wolf (Bangkok, Thailand)
Charles Lin (Roivant Discovery)
G. Andrés Cisneros (UNT)
Ali Rahnamoun (Michigan State)
Akhil Shajan (Michigan State)
Madushanka Manathunga (Michigan State)
Joshua T. Berryman (Uni. Luxembourg)
Robert E. Duke (UNT)
Nikolai R. Skrynnikov (Purdue, SPbU)
Oleg Mikhailovskii (Purdue, SPbU)
Yi Xue (Tsinghua)
Sergei A. Izmailov (SPbU)
Koushik Kasavajhala (Stony Brook)
Kellon Belfon (Roivant Discovery)
Jana Shen (Maryland)
Robert Harris (Maryland)
Alexey Onufriev (Virginia Tech)
Saeed Izadi (Virginia Tech, Genentech)
Yeyue Xiong (Virginia Tech)
Xiongwu Wu (NIH)
Holger Gohlke (Düsseldorf/FZ Jülich)
Stephan Schott-Verdugo (FZ Jülich)
Ruxi Qi (UC Irvine)
Haixin Wei (UC Irvine)
Shiji Zhao (UC Irvine)
Edward King (UC Irvine)
George Giambasu (Merck)
Jian Liu (Peking Univ.)
Hai Nguyen (Schrodinger)
Scott R. Brozell (Rutgers)
Andriy Kovalenko (NINT)
Mike Gilson (UC San Diego)
Ido Ben-Shalom (UC San Diego)
Tom Kurtzman (CUNY)
Sergio Pantano (Inst. Pasteur, Uruguay)
Matias Machado (Inst. Pasteur, Uruguay)
H. Metin Aktulga (Michigan State)
Mehmet Cagri Kaymak (Michigan State)
Kurt A. O’Hearn (Michigan State)
Peter A. Kollman (UC San Francisco)
For more information, please visit https://ambermd.org/contributors.html
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• When citing Amber 2022 (comprised of AmberTools22 and Amber22) in the literature, the following citation
should be used:
D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, 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, K. Kasavajhala, M.C. Kaymak, E. King, A. Ko-
valenko, 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,
A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang,
H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022,
University of California, San Francisco.
• Peter Kollman died unexpectedly in May, 2001. We dedicate Amber to his memory.
• Cover illustration: Representation of DNA polymerase (blue) active site from bacteriophage RB69, contain-
ing duplex DNA with bound thymidine-triphosphate. In yellow are two Mg2+ ions, with the coordinating
protein residues shown as sticks (three aspartic acid sidechains and the protein backbone). Snapshot from
MD simulations of crystal structure (PDB ID: 1IG9). Figure by Lucy Fallon.
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Contents
Contents 5
I. Introduction and Installation 11
1. Introduction 13
1.1. Information flow in Amber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.2. List of programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2. Installation 21
2.1. Basic installation guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.2. The cmake build system in Amber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.3. Python in Amber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.4. Applying Updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.5. Contacting the developers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
II. Amber force fields 31
3. Molecular mechanics force fields 33
3.1. Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.2. Nucleic acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3.3. Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.4. Lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.5. Solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.6. Ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.7. Modified amino acids and nucleotides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.8. Force fields related to semi-empirical QM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.9. The GAL17 force field for water over platinum . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.10. Fluorescent dyes: AMBER-DYES in AMBER force field files . . . . . . . . . . . . . . . . . . . 58
3.11. Coarse-grained and multiscale simulations using the SIRAH force field . . . . . . . . . . . . . . 60
3.12. Obsolete force field files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
4. The Generalized Born/Surface Area Model 67
4.1. GB/SA input parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
4.2. ALPB (Analytical Linearized Poisson-Boltzmann) . . . . . . . . . . . . . . . . . . . . . . . . . 72
5. GBNSR6 75
5.1. GB equations available in gbnsr6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
5.2. Numerical implementation of the R6 integral . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
5.3. Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
6. PBSA 79
6.1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
6.2. Usage and keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
6.3. Example inputs and demonstrations of functionalities . . . . . . . . . . . . . . . . . . . . . . . . 91
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