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Amber 12 Reference Manual 2 Amber 12 Reference Manual Principal Contributors to the Current Codes

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Amber 12 Reference Manual 2 Amber 12 Reference Manual Principal Contributors to the Current Codes Amber 12 Reference Manual 2 Amber 12 Reference Manual Principal contributors to the current codes: David A. Case (Rutgers University) Jian Liu (Berkeley) Tom Darden (OpenEye) Xiongwu Wu (NIH) Thomas E. Cheatham III (Utah) Scott R. Brozell (Rutgers) Carlos Simmerling (Stony Brook) Thomas Steinbrecher (Karlsruhe) Junmei Wang (UT Southwestern Medical Center) Holger Gohlke (Düsseldorf) Robert E. Duke (NIEHS and UNC-Chapel Hill) Qin Cai (UC Irvine) Ray Luo (UC Irvine) Xiang Ye (UC Irvine) Ross C. Walker (SDSC, UCSD) Jun Wang (UC Irvine) Wei Zhang (UT Houston) Meng-Juei Hsieh (UC Irvine) Kenneth M. Merz (Florida) Guanglei Cui (Stony Brook) Benjamin P. Roberts (Florida) Daniel R. Roe (Rutgers University) Seth Hayik (Florida) David H. Mathews (Rochester) Adrian Roitberg (Florida) Matthew G. Seetin (Rochester) Gustavo Seabra (Recife, Brazil) Romelia Salomon-Ferrer (SDSC, UCSD) Jason Swails (Florida) Celeste Sagui (North Carolina State) Andreas W. Götz (SDSC, UCSD) Volodymyr Babin (North Carolina State) István Kolossváry (Budapest and D.E. Shaw) Tyler Luchko (Rutgers University) Kim F. Wong (Pitt) Sergey Gusarov (NINT) Francesco Paesani (UC San Diego) Andriy Kovalenko (NINT) Jiri Vanicek (EPL-Lausanne) Peter A. Kollman (UC San Francisco) Romain M. Wolf (Novartis) Additional key contributors to earlier versions: David A. Pearlman (UC San Francisco) Bing Wang (Florida) Robert V. Stanton (UC San Francisco) Chunhu Tan (UC Irvine) Jed Pitera (UC San Francisco) Lijiang Yang (UC Irvine) Irina Massova (UC San Francisco) Christian Schafmeister (Pitt) Ailan Cheng (Penn State) Wilson S. Ross (UC San Francisco) James J. Vincent (Penn State) Randall Radmer (UC San Francisco) Paul Beroza (Telik) George L. Seibel (UC San Francisco) Vickie Tsui (TSRI) James W. Caldwell (UC San Francisco) Mike Crowley (NREL) U. Chandra Singh (UC San Francisco) John Mongan (UC San Diego) Paul Weiner (UC San Francisco) For more information, please visit http://ambermd.org/contributors 1 Acknowledgments Research support from DARPA, NIH and NSF for Peter Kollman is gratefully acknowledged, as is support from NIH, NSF, ONR and DOE for David Case. Use of the facilities of the UCSF Computer Graphics Laboratory (Thomas Ferrin, PI) is appreciated. The pseudocontact shift code was provided by Ivano Bertini of the University of Florence. We thank Chris Bayly and Merck-Frosst, Canada for permission to include charge increments for the AM1-BCC charge scheme. Many people helped add features to various codes; these contributions are described in the documentation for the individual programs; see also http://ambermd.org/contributors.html. Recommended Citations: • When citing Amber 12 in the literature, the following citation should be used: D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Götz, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco. The history of the codes and a basic description of the methods can be found in three papers: • D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free en- ergy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91, 1-41 (1995). • D.A. Case, T. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005). • R. Salomon-Ferrer, D.A. Case, R. C Walker. An overview of the Amber Biomolecular Simulation Package. WIREs Comput. Mol. Sci. in press (2012). Peter Kollman died unexpectedly in May, 2001. We dedicate Amber to his memory. Cover Illustration The cover image represents the allosteric changes in the transcriptional repressor protein Staphylococcus aureus CzrA upon binding of Zn(II). As Zn(II) binds DNA bound apo-CzrA (upper right image) the DNA binding affinity is reduced by 4 orders of magnitude and the struc- ture of CzrA switches from a +“closed” conformation to an “open” conformation facilitating its release from DNA (lower left image). See http://pubs.acs.org/doi/abs/10.1021/ja208047b. Image created by M. Nihan Ucisik, Dhruva Chakravorty and Kenneth M. Merz, Jr. 2 Contents Contents 3 1 Introduction 9 1.1 What to read next.................................9 1.2 Installation of Amber 12............................. 10 1.3 Basic tutorials................................... 10 2 Sander basics 13 2.1 Introduction.................................... 13 2.2 File usage..................................... 15 2.3 Example input files................................ 16 2.4 Overview of the information in the input file................... 17 2.5 General minimization and dynamics parameters................. 17 2.5.1 General flags describing the calculation................. 17 2.5.2 Nature and format of the input...................... 18 2.5.3 Nature and format of the output..................... 19 2.5.4 Frozen or restrained atoms........................ 21 2.5.5 Energy minimization........................... 22 2.5.6 Molecular dynamics........................... 22 2.5.7 Temperature regulation.......................... 23 2.5.8 Pressure regulation............................ 25 2.5.9 SHAKE bond length constraints..................... 26 2.5.10 Water cap................................. 27 2.5.11 NMR refinement options......................... 28 2.5.12 EMAP constraints............................ 29 2.6 Potential function parameters........................... 29 2.6.1 Generic parameters............................ 29 2.6.2 Particle Mesh Ewald........................... 31 2.6.3 Using IPS for the calculation of nonbonded interactions........ 33 2.6.4 Extra point options............................ 34 2.6.5 Polarizable potentials........................... 35 2.6.6 Dipole Printing.............................. 36 2.6.7 Detailed MPI Timings.......................... 36 2.7 Varying conditions................................ 37 2.8 File redirection commands............................ 41 2.9 Getting debugging information.......................... 42 3 CONTENTS 3 Force field modifications 47 3.1 The Generalized Born/Surface Area Model................... 47 3.1.1 GB/SA input parameters......................... 50 3.1.2 ALPB (Analytical Linearized Poisson-Boltzmann)........... 53 3.2 PBSA....................................... 54 3.3 Reference Interaction Site Model of Molecular Solvation............ 55 3.3.1 Multiple Time Step Methods for 3D-RISM............... 55 3.3.2 3D-RISM in sander ........................... 56 3.4 Empirical Valence Bond............................. 63 3.4.1 Introduction................................ 63 3.4.2 General usage description........................ 65 3.4.3 Biased sampling............................. 67 3.4.4 Quantization of nuclear degrees of freedom............... 69 3.4.5 Distributed Gaussian EVB........................ 70 3.4.6 EVB input variables and interdependencies............... 73 3.5 The AMOEBA force field............................. 78 3.6 QM/MM calculations: Semi-empirical methods................. 80 3.6.1 The hybrid QM/MM potential...................... 80 3.6.2 The QM/MM interface and link atoms.................. 82 3.6.3 A reformulated QM/MM interface for PM3............... 83 3.6.4 Generalized Born implicit solvent.................... 84 3.6.5 Ewald and PME............................. 84 3.6.6 Hints for running successful QM/MM calculations........... 85 3.6.7 General QM/MM &qmmm Namelist Variables............. 86 3.6.8 Link Atom Specific QM/MM &qmmm Namelist Variables....... 90 3.7 QM/MM calculations: ab initio and DFT methods................ 91 3.7.1 Theory.................................. 92 3.7.2 General Remarks............................. 94 3.7.3 Limitations................................ 94 3.7.4 Performance Considerations....................... 95 3.7.5 Parallelization.............................. 95 3.7.6 Usage................................... 95 3.8 Charge Relocation................................ 106 3.8.1 Preparing Input Files for Charge Relocation............... 107 4 Sampling and free energies 113 4.1 Thermodynamic integration............................ 113 4.1.1 Basic inputs for thermodynamic integration............... 114 4.1.2 Softcore Potentials in Thermodynamic Integration........... 118 4.1.3 Collecting potential energy differences for FEP calculations...... 120 4.2 Umbrella sampling................................ 121 4.3 Self-Guided Langevin dynamics......................... 122 4.4 Targeted MD................................... 124 4.5 Multiply-Targeted MD (MTMD)......................... 126 4.5.1 Variables in the &tgt namelist:..................... 126 4 CONTENTS 4.6 Steered Molecular Dynamics (SMD) and the Jarzynski Relationship...... 128 4.6.1 Background................................ 128 4.6.2 Implementation and usage........................ 129 4.7 Replica Exchange Molecular Dynamics (REMD)................ 130 4.7.1 Running REMD simulations....................... 131 4.7.2 Restarting
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