Amber 8 Users' Manual

320 Pages·2004·0.91 MB·English

Amber 8
Users’ Manual

AMBER 8
Users’ Manual
Principal contributors to the current codes:
David A. Case (The Scripps Research Institute)
TomDarden (NIEHS)
Thomas E. Cheatham III (University of Utah)
Carlos Simmerling (StonyBrook)
Junmei Wang (Encysive Pharmaceuticals)
Robert E. Duke(University of North Carolina)
Ray Luo (UC Irvine)
Kenneth M. Merz (Penn State)
Bing Wang (Penn State)
David A. Pearlman (UC San Francisco)
MikeCrowley(TSRI)
Scott Brozell (TSRI)
Vickie Tsui (TSRI)
Holger Gohlke(TSRI, J.W.Goethe-Universität)
John Mongan (UC San Diego)
Viktor Hornak (StonyBrook)
Guanglei Cui (StonyBrook)
Paul Beroza (Telik)
Christian Schafmeister (UC San Francisco)
James W.Caldwell (UC San Francisco, Stanford)
Wilson S. Ross (UC San Francisco)
Peter A. Kollman (UC San Francisco)
Additional key contributors to earlier versions:
Robert V.Stanton (UC San Francisco)
Jed Pitera (UC San Francisco)
Irina Massova (UC San Francisco)
Ailan Cheng (Penn State)
James J. Vincent (Penn State)
Randall Radmer (UC San Francisco)
George L. Seibel (UC San Francisco)
U. Chandra Singh (UC San Francisco)
Paul Weiner (UC San Francisco)
Additional key people involved in force field development:
Piotr Cieplak (Accerlys)
Yong Duan (University of Delaware)
Rob Woods (University of Georgia)
Karl Kirschner (University of Georgia)
Sarah M. Tschampel (University of Georgia)
Alexey Onufriev(Virginia Tech.)
Christopher Bayly (Merck-Frost)
Wendy Cornell (UC San Francisco, Novartis)
Scott Weiner (UC San Francisco)
Page 2
Acknowledgments
We acknowledge the generous cooperation of Wilfred van Gunsteren, whose molecular dynamics
code was used as the basis of the md modules in version 2.0. Weare also pleased to acknowledge
Rad Olson and Bill Swope at IBM Almaden Center, whose contributions were instrumental in
developing the better vector optimized non-bonded routines first released in version 3, revision A.
Research support from DARPA, NIH and NSF for Peter Kollman is gratefully acknowledged, as
is support from NIH, NSF 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 pro-
vided 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 documenta-
tion for the individual programs.
Recommended Citations:
When citing Amber Version 8 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, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S.Brozell, V.Tsui, H. Gohlke, J.
Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and
P.A. Kollman (2004), AMBER 8, University of California, San Francisco.
The history of the codes and a basic description of the methods can be found in:
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
energy calculations to simulate the structural and energetic properties of molecules.
Comp. Phys. Commun.91,1-41 (1995).
Peter Kollman died unexpectedly in May,2001. Wededicate Amber to his memory.
Cover Illustration
The cover image shows the complex between duplex DNA and the formamidopyrimidine-DNA
glycosylase (called Fpg or MutM) involved in repair of oxidatively damaged bases. The coordi-
nates represent a covalently trapped complex following removal of 8-oxo-G, and were obtained
from X-ray crystallography (pdb code 1K82). The enzyme is shown as a schematic and the DNA
duplex is shown with solvent-accessible surface and heavy atoms for the bases. The image was
produced by Asim Okur,Adrian Roitbergand Carlos Simmerling.
2/25/04
Table of Contents i
Table of Contents
1. Introduction ..................................................................................................................... 3
1.1. What to read next ..................................................................................................... 3
1.2. Information flowinAmber ...................................................................................... 4
1.2.1. Preparatory programs ...................................................................................... 5
1.2.2. Simulation programs ....................................................................................... 5
1.2.3. Analysis programs .......................................................................................... 6
1.3. Installation of Amber 8 ............................................................................................ 6
1.3.1. More information on parallel machines or clusters ........................................ 8
1.3.2. Installing Non-Standard Features ................................................................... 9
1.3.3. Installing on Windows .................................................................................... 9
1.3.4. Testing ............................................................................................................. 9
1.3.5. Memory Requirements.................................................................................... 10
1.3.6. Notes for users of previous versions of Amber............................................... 10
1.4. Basic tutorials ........................................................................................................... 11
2. Specifying a force field .................................................................................................... 14
2.1. Description of the database files .............................................................................. 15
2.2. Specifying which force field you want in LEaP ...................................................... 17
2.3. The Duan et al. (2003) force field ............................................................................ 18
2.4. 1999 and 2002 force fields ....................................................................................... 18
2.5. The Cornell et al. (1994) force field......................................................................... 19
2.6. The Weiner et al. (1984,1986) force fields............................................................... 20
2.7. Glycam-04 force field for carbohydrates ................................................................. 20
2.7.1. Notes on the naming of Prep files ................................................................... 21
2.7.2. Carbohydrate Naming Convention in Glycam-04 .......................................... 22
2.7.3. Building a polysaccharaide in LEaP ............................................................... 26
2.8. Ions ........................................................................................................................... 28
2.9. Solvent models ......................................................................................................... 28
3. LEaP ................................................................................................................................. 30
3.1. Introduction .............................................................................................................. 30
3.2. Concepts ................................................................................................................... 30
3.2.1. Commands ...................................................................................................... 31
3.2.2. Variables .......................................................................................................... 31
3.2.3. Objects ............................................................................................................ 32
3.2.3.1. NUMBERs ............................................................................................. 32
3.2.3.2. STRINGs ................................................................................................ 32
3.2.3.3. LISTs ...................................................................................................... 32
3.2.3.4. PARMSETs (Parameter Sets) ................................................................ 32
3.2.3.5. ATOMs ................................................................................................... 32
Table of Contents ii
3.2.3.6. RESIDUEs ............................................................................................. 34
3.2.3.7. UNITs .................................................................................................... 35
3.2.3.8. Complexobjects and accessing subobjects............................................ 36
3.3. Starting LEaP ........................................................................................................... 38
3.3.1. Verbosity ......................................................................................................... 38
3.3.2. Log File ........................................................................................................... 38
3.4. Using LEaP .............................................................................................................. 39
3.4.1. Universe Editor ............................................................................................... 39
3.4.2. Unit Editor ...................................................................................................... 40
3.4.2.1. Unit Editor Menu Bar ............................................................................ 40
3.4.2.2. Unit Editor Manipulation Buttons ......................................................... 42
3.4.2.3. Unit Editor Elements Buttons ................................................................ 43
3.4.2.4. Unit Editor Viewing Window ................................................................ 44
3.4.3. Atom Properties Editor ................................................................................... 45
3.4.4. Parmset Editor ................................................................................................. 45
3.5. Basic instructions for using LEaP with AMBER .................................................... 45
3.5.1. Building a Molecule For Molecular Mechanics ............................................. 45
3.5.2. Amino Acid Residues ..................................................................................... 47
3.5.3. Nucleic Acid Residues .................................................................................... 48
3.5.4. Miscellaneous Residues .................................................................................. 48
3.6. Commands ............................................................................................................... 49
3.6.1. add ................................................................................................................... 49
3.6.2. addAtomTypes ................................................................................................ 50
3.6.3. addIons ............................................................................................................ 51
3.6.4. addIons2 .......................................................................................................... 51
3.6.5. addPath ............................................................................................................ 51
3.6.6. addPdbAtomMap ............................................................................................ 52
3.6.7. addPdbResMap ............................................................................................... 52
3.6.8. alias ................................................................................................................. 53
3.6.9. bond ................................................................................................................. 53
3.6.10. bondByDistance ............................................................................................ 53
3.6.11. center ............................................................................................................. 54
3.6.12. charge ............................................................................................................ 54
3.6.13. check ............................................................................................................. 54
3.6.14. combine ......................................................................................................... 55
3.6.15. copy ............................................................................................................... 55
3.6.16. createAtom .................................................................................................... 56
3.6.17. createParmset ................................................................................................ 56
3.6.18. createResidue ................................................................................................ 56
3.6.19. createUnit ...................................................................................................... 57
3.6.20. deleteBond .................................................................................................... 57
3.6.21. desc ............................................................................................................... 57
Table of Contents iii
3.6.22. edit ................................................................................................................. 58
3.6.23. groupSelectedAtoms ..................................................................................... 58
3.6.24. help ................................................................................................................ 59
3.6.25. impose ........................................................................................................... 59
3.6.26. list .................................................................................................................. 60
3.6.27. loadAmberParams ......................................................................................... 60
3.6.28. loadAmberPrep ............................................................................................. 61
3.6.29. loadOff .......................................................................................................... 61
3.6.30. loadMol2 ....................................................................................................... 62
3.6.31. loadPdb ......................................................................................................... 62
3.6.32. loadPdbUsingSeq .......................................................................................... 63
3.6.33. logFile ........................................................................................................... 63
3.6.34. measureGeom ............................................................................................... 64
3.6.35. quit ................................................................................................................ 65
3.6.36. remove ........................................................................................................... 65
3.6.37. saveAmberParm ............................................................................................ 65
3.6.38. saveAmberParmPol ....................................................................................... 66
3.6.39. saveAmberParmPert ...................................................................................... 66
3.6.40. saveAmberParmPolPert ................................................................................ 67
3.6.41. saveOff .......................................................................................................... 67
3.6.42. savePdb ......................................................................................................... 67
3.6.43. scaleCharges ................................................................................................. 67
3.6.44. sequence ........................................................................................................ 68
3.6.45. set .................................................................................................................. 69
3.6.46. setBox ........................................................................................................... 71
3.6.47. solvateBox ..................................................................................................... 71
3.6.48. solvateCap ..................................................................................................... 72
3.6.49. solvateDontClip ............................................................................................ 73
3.6.50. solvateOct ..................................................................................................... 74
3.6.51. solvateShell ................................................................................................... 74
3.6.52. source ............................................................................................................ 75
3.6.53. transform ....................................................................................................... 75
3.6.54. translate ......................................................................................................... 76
3.6.55. verbosity ........................................................................................................ 76
3.6.56. zMatrix .......................................................................................................... 76
4. Antechamber ................................................................................................................... 78
4.1. Principal programs ................................................................................................... 79
4.1.1. antechamber .................................................................................................... 79
4.1.2. parmchk........................................................................................................... 81
4.2. A simple example for antechamber ......................................................................... 81
4.3. Programs called by antechamber ............................................................................. 84
4.3.1. atomtype .......................................................................................................... 84
Table of Contents iv
4.3.2. am1bcc ............................................................................................................ 85
4.3.3. bondtype .......................................................................................................... 85
4.3.4. prepgen ............................................................................................................ 86
4.3.5. espgen ............................................................................................................. 86
4.3.6. respgen ............................................................................................................ 87
4.4. Miscellaneous programs .......................................................................................... 87
4.4.1. crdgrow ........................................................................................................... 87
4.4.2. parmcal ............................................................................................................ 88
4.4.3. database ........................................................................................................... 88
5. Sander .............................................................................................................................. 89
5.1. Introduction. ............................................................................................................ 89
5.2. Credits. .................................................................................................................... 91
5.3. File usage. ............................................................................................................... 92
5.4. Example input files. ................................................................................................ 92
5.5. Overviewofthe information in the input file. ........................................................ 94
5.6. SECTION ONE: General minimization and dynamics parameters. ...................... 95
5.6.1. General flags describing the calculation. ....................................................... 95
5.6.2. Nature and format of the input. ...................................................................... 95
5.6.3. Nature and format of the output. .................................................................... 96
5.6.4. Potential function. .......................................................................................... 98
5.6.5. Generalized Born/Surface Area options. ....................................................... 99
5.6.6. Frozen or restrained atoms. ............................................................................ 101
5.6.7. Energy minimization. ..................................................................................... 102
5.6.8. Molecular dynamics. ...................................................................................... 102
5.6.9. Temperature regulation. ................................................................................. 103
5.6.10. Pressure regulation. ...................................................................................... 105
5.6.11. SHAKE bond length constraints. ................................................................. 105
5.6.12. Water cap. .................................................................................................... 106
5.6.13. NMR refinement options. ............................................................................. 106
5.6.14. Particle Mesh Ewald. ................................................................................... 107
5.6.15. Extra point options. ...................................................................................... 109
5.6.16. Polarizable potentials. .................................................................................. 111
5.6.17. Dipole Printing .............................................................................................. 111
5.7. SECTION TWO: Weight change information. ..................................................... 113
5.8. SECTION THREE: File redirection commands. .................................................... 118
5.9. SECTION FOUR: Distance, angle and torsional restraints. .................................. 119
5.10. SECTION FIVE: NOESY volume restraints. ...................................................... 124
5.11. SECTION SIX: Chemical shift restraints. ........................................................... 126
5.12. SECTION SEVEN: Direct dipolar coupling restraints ......................................... 129
5.13. Free energies using thermodynamic integration. .................................................. 132
5.14. Targeted MD .......................................................................................................... 135
5.15. Potentials of mean force using umbrella sampling. .............................................. 137
Table of Contents v
5.16. Poisson-Boltzmann dynamics. .............................................................................. 139
5.17. QM/MM calculations ............................................................................................. 141
5.17.1. Coupled Potential Namelist Variables .......................................................... 141
5.17.2. Coupled Potential Formatted Input ............................................................... 142
5.17.2.1. Lines for PMF runs .............................................................................. 142
5.17.2.2. Lines for all coupled potential runs ..................................................... 143
5.17.3. Control Files for Coupled Potential Simulations .......................................... 143
5.18. Replica-Exchange. ................................................................................................ 145
5.18.1. Multisander REM .......................................................................................... 145
5.18.1.1. Restarting REM simulations ................................................................ 147
5.18.1.2. Contentof the output files ................................................................... 147
5.18.1.3. Major Changes from sander ................................................................. 148
5.18.1.4. Example ............................................................................................... 149
5.18.2. Multiscale Modeling Tools in Structural Biology ........................................ 149
5.19. Constant pH calculations ....................................................................................... 151
5.19.1. Background ................................................................................................... 151
5.19.2. Preparing a system for constant pH .............................................................. 151
5.19.3. Running at constant pH ................................................................................. 152
5.19.4. Analyzing constant pH simulations .............................................................. 153
5.19.5. Extending constant pH to additional titratable groups .................................. 154
5.19.5.1. Defining charge sets ............................................................................. 155
5.19.5.2. Calculating relative energies ................................................................ 155
5.19.5.3. Testing the titratable group definitions ................................................ 155
5.20. OverviewofNMR refinement using SANDER. ................................................... 157
5.20.1. Preparing restraint files for Sander ............................................................... 158
5.20.2. Preparing distance restraints: makeDIST_RST. ........................................... 158
5.20.3. Preparing torsion angle restraints: makeANG_RST ..................................... 162
5.20.4. Chirality restraints: makeCHIR_RST ........................................................... 164
5.20.5. Direct dipolar coupling restraints: makeDIP_RST ....................................... 164
5.20.6. Getting summaries of NMR violations ......................................................... 165
5.20.7. Time-averaged restraints. ............................................................................. 165
5.20.8. Multiple copies refinement using LES .......................................................... 166
5.20.9. Some sample input files ................................................................................ 167
5.21. Getting debugging information .............................................................................. 174
6. PMEMD (Particle Mesh Ewald Molecular Dynamics) ............................................... 178
6.1. Introduction. ............................................................................................................ 178
6.2. Functionality ............................................................................................................ 178
6.3. Newvariables ........................................................................................................... 180
6.4. Installation ................................................................................................................ 181
6.5. Acknowledgements .................................................................................................. 182
7. LES ................................................................................................................................... 183
7.1. Preparing to use LES with AMBER ........................................................................ 183
Table of Contents vi
7.2. Using the ADDLES program ................................................................................... 184
7.3. More information on the ADDLES commands and options ................................... 187
7.4. Using the newtopology/coordinate files with SANDER ........................................ 188
7.5. Using LES with the Generalized Born solvation model .......................................... 189
7.6. Case studies: Examples of application of LES ........................................................ 189
7.6.1. Enhanced sampling for individual functional groups: Glucose. .................... 189
7.6.2. Enhanced sampling for a small region: Application of LES to a nucleic
acid loop ....................................................................................................................... 190
7.6.3. Improving conformational sampling in a small peptide ................................. 191
7.7. Unresolved issues with LES in AMBER ................................................................. 193
8. ptraj .................................................................................................................................. 194
8.1. ptraj command prerequisites .................................................................................... 195
8.2. ptraj input/output commands ................................................................................... 196
8.3. ptraj commands that modify the state ...................................................................... 197
8.4. ptrajactioncommands ............................................................................................. 198
8.5. Correlation and fluctuation facility .......................................................................... 205
8.6. Examples .................................................................................................................. 209
8.7. Hydrogen bonding facility ....................................................................................... 211
8.8. rdparm ...................................................................................................................... 212
9. MM-PBSA ....................................................................................................................... 218
9.1. General instructions ................................................................................................. 218
9.2. Preparing the input file ............................................................................................. 219
9.3. Auxiliary programs used by MM-PBSA ................................................................. 227
10. Nmode ............................................................................................................................ 228
10.1. Introduction ............................................................................................................ 228
10.2. General description ................................................................................................ 228
10.3. Files ........................................................................................................................ 229
10.4. Input description .................................................................................................... 229
11. Miscellaneous................................................................................................................. 233
11.1. Resp ........................................................................................................................ 233
11.2. nucgen .................................................................................................................... 236
11.3. ambpdb ................................................................................................................... 239
11.4. protonate ................................................................................................................ 241
11.5. ambmask ................................................................................................................ 243
11.6. pol_h and gwh ........................................................................................................ 246
11.7. intense .................................................................................................................... 248
11.8. spectrum ................................................................................................................. 250
11.9. fantasian ................................................................................................................. 251
11.10. pbsa ...................................................................................................................... 252
12. Science background ...................................................................................................... 254
12.1. Parameter Development ......................................................................................... 254
12.2. Charge Fitting Philosophy ..................................................................................... 262