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Amber 14 Reference Manual Principal Contributors to the Current Codes

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Amber 14 Reference Manual Principal Contributors to the Current Codes Amber 14 Reference Manual Principal contributors to the current codes: David A. Case (Rutgers) Andreas W. Götz (SDSC, UCSD) Tom Darden (OpenEye) István Kolossváry (Budapest and D.E. Shaw) Thomas E. Cheatham III (Utah) Francesco Paesani (UCSD)Jian Liu (Berkeley) Carlos Simmerling (Stony Brook) Xiongwu Wu (NIH) Adrian Roitberg (Florida) Thomas Steinbrecher (Karlsruhe) Junmei Wang (UT Southwestern Medical Center) Holger Gohlke (Düsseldorf) Robert E. Duke (NIEHS and UNC-Chapel Hill) Nadine Homeyer (Düsseldorf) Ray Luo (UC Irvine) Qin Cai (UC Irvine) Daniel R. Roe (Utah) Wes Smith (UC Irvine) Ross C. Walker (SDSC, UCSD) Dave Mathews (Rochester) Scott LeGrand (Amazon) Romelia Salomon-Ferrer (SDSC, UCSD) Jason Swails (Rutgers) Celeste Sagui (North Carolina State) David Cerutti (Rutgers) Volodymyr Babin (North Carolina State) Joe Kaus (UCSD) Tyler Luchko (Rutgers) Robin Betz (UCSD) Sergey Gusarov (NINT) Romain M. Wolf (Novartis) Andriy Kovalenko (NINT) Kenneth M. Merz (Michigan State) Josh Berryman (U. of Luxembourg) Gustavo Seabra (Recife, Brazil) Peter A. Kollman (UC San Francisco) Pawel Janowski (Rutgers) For more information, please visit http://ambermd.org/contributors 3 Acknowledgments Research support from DARPA, NIH, ONR, DOE and NSF is gratefully acknowledged, along with support from NVIDIA, Amazon and Exxact. 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 Citation: • When citing Amber 14 in the literature, the following citation should be used: D.A. Case, V. Babin, J.T. Berryman, R.M. Betz, Q. Cai, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, H. Gohlke, A.W. Goetz, S. Gusarov, N. Homeyer, P. Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T.S. Lee, S. LeGrand, T. Luchko, R. Luo, B. Madej, K.M. Merz, F. Paesani, D.R. Roe, A. Roitberg, C. Sagui, R. Salomon-Ferrer, G. Seabra, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu and P.A. Kollman (2014), AMBER 14, University of California, San Francisco. Peter Kollman died unexpectedly in May, 2001. We dedicate Amber to his memory. Notes • We thank Chris Bayly and Merck-Frosst, Canada for permission to include charge increments for the AM1- BCC charge scheme. • Some of the force field routines were adapted from similar routines in the MOIL program package: R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker, C. Keasar, J. Zhang and A. Ulitsky, "MOIL: A program for simulations of macromolecules" Comp. Phys. Commun. 91, 159-189 (1995). • The cifparse routines to deal with mmCIF formatted files were written by John Westbrook, and are dis- tributed with permission. See cifparse/README for details. Cover illustration: The cover shows all atom bilayer self assembly of 128 DOPC phospholipids simulated using the GPU version of pmemd. The lipid molecules were represented with the Lipid14 force field parameters, along with TIP3P waters and 0.15 M KCl. The lipids are presented as stick models, with the head group phosphorus atoms highlighted as orange spheres. Water and ions have been removed for clarity. Taken from Skjevik, Å. A.; Madej, B. D.; Dickson, C. J.; Teigen, K.; Walker, R.C.; Gould, I.R., J. Am. Chem. Soc. 2014, in review. 4 Contents Contents 5 I. Introduction and Installation 13 1. Introduction 15 1.1. Information flow in Amber...................................... 15 1.2. List of programs............................................ 18 2. Installation 21 2.1. Applying Updates........................................... 23 2.2. Contacting the developers....................................... 25 II. Amber force fields 27 3. Molecular mechanics force fields 29 3.1. Specifying which force field you want in LEaP........................... 29 3.2. The ff14SB force field........................................ 30 3.3. The ff14ipq protein force field.................................... 32 3.4. The Duan et al. (2003) force field.................................. 33 3.5. The Yang et al. (2003) united-atom force field............................ 34 3.6. Force fields related to semi-empirical QM.............................. 34 3.7. The GLYCAM force fields for carbohydrates and lipids....................... 34 3.8. Lipid Force Fields........................................... 42 3.9. Ions.................................................. 44 3.10. Solvent models............................................ 46 3.11. CHAMBER.............................................. 47 3.12. Obsolete force field files....................................... 52 4. The Generalized Born/Surface Area Model 57 4.1. GB/SA input parameters....................................... 59 4.2. ALPB (Analytical Linearized Poisson-Boltzmann)......................... 61 5. PBSA 65 5.1. Introduction.............................................. 65 5.2. Usage and keywords......................................... 68 5.3. Example inputs and demonstrations of functionalities........................ 76 5.4. Visualization functions in pbsa .................................... 79 5.5. pbsa in sander and NAB....................................... 86 6. Reference Interaction Site Model 89 6.1. Introduction.............................................. 89 6.2. Practical Considerations....................................... 94 6.3. Work Flow.............................................. 95 6.4. rism1d................................................. 95 5 CONTENTS 6.5. 3D-RISM in NAB ........................................... 98 6.6. rism3d.snglpnt ........................................... 101 6.7. 3D-RISM in sander.......................................... 103 7. Empirical Valence Bond 111 7.1. Introduction.............................................. 111 7.2. General usage description....................................... 112 7.3. Biased sampling............................................ 115 7.4. Quantization of nuclear degrees of freedom............................. 117 7.5. Distributed Gaussian EVB...................................... 117 7.6. EVB input variables and interdependencies............................. 119 8. sqm: Semi-empirical quantum chemistry 125 8.1. Available Hamiltonians........................................ 125 8.2. Dispersion and hydrogen bond correction.............................. 126 8.3. Usage................................................. 127 9. QM/MM calculations 133 9.1. Built-in semiempirical NDDO methods and SCC-DFTB...................... 133 9.2. Interface for ab initio and DFT methods............................... 142 9.3. Adaptive solvent QM/MM simulations................................ 153 9.4. Adaptive buffered force-mixing QM/MM.............................. 158 9.5. SEBOMD: SemiEmpirical Born-Oppenheimer Molecular Dynamics................ 165 10. paramfit 171 10.1. Usage................................................. 172 10.2. The Job Control File......................................... 173 10.3. Multiple molecule fits......................................... 179 10.4. Fitting Forces............................................. 179 10.5. Examples............................................... 180 III. System preparation 183 11. Preparing PDB Files 185 11.1. Cleaning up Protein PDB Files for AMBER............................. 185 11.2. Residue naming conventions..................................... 186 11.3. Chains, Residue Numbering, Missing Residues........................... 187 11.4. pdb4amber.............................................. 187 11.5. reduce................................................. 190 12. LEaP 191 12.1. Introduction.............................................. 191 12.2. Concepts............................................... 191 12.3. Running LEaP............................................. 195 12.4. Basic instructions for using LEaP to build molecules........................ 200 12.5. Commands.............................................. 201 12.6. Building oligosaccharides, lipids and glycoproteins......................... 217 13. Reading and modifying Amber parameter files 225 13.1. Understanding Amber parameter files................................ 225 13.2. ParmEd................................................ 233 6 CONTENTS 14. Antechamber and GAFF 255 14.1. Principal programs.......................................... 255 14.2. A simple example for antechamber.................................. 259 14.3. Using the components.cif file from the PDB............................. 262 14.4. Programs called by antechamber................................... 262 14.5. Miscellaneous programs....................................... 266 14.6. New Development of Antechamber And GAFF........................... 268 14.7. Metal Center Parameter Builder (MCPB).............................. 269 15. Setting up crystal simulations 271 15.1. UnitCell................................................ 271 15.2. PropPDB............................................... 271 15.3. AddToBox............................................... 271 15.4. ChBox................................................. 273 16. Using the AMOEBA Force Field with AMBER 275 16.1. Installing TINKER.......................................... 275 16.2. Preparing the system with TINKER................................. 276 IV. Running simulations 279 17. sander 281 17.1. Introduction.............................................. 281 17.2. File usage............................................... 282 17.3. Example input
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