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ambertool手册.pdf
Contents
Getting started
Information flow in Amber
Installation
Combining AmberTools13 with Amber11 or Amber10
Testing the installation
Applying Updates
Contacting the developers
List of programs
Specifying a force field
Specifying which force field you want in LEaP
The ff12SB force field
The AMOEBA potentials
The Duan et al. (2003) force field
The Yang et al. (2003) united-atom force field
Force fields related to semi-empirical QM
The GLYCAM force fields for carbohydrates and lipids
Lipid Force Fields
Ions
Solvent models
CHAMBER
Obsolete force field files
Reading and modifying Amber parameter files
Understanding Amber parameter files
ParmEd
paramfit
LEaP
Introduction
Concepts
Running LEaP
Basic instructions for using LEaP to build molecules
Commands
Building oligosaccharides and lipids
Antechamber and MCPB
Principal programs
A simple example for antechamber
Programs called by antechamber
Miscellaneous programs
New Development of Antechamber And GAFF
Metal Center Parameter Builder (MCPB)
amberlite: Some AmberTools-Based Utilities
Introduction
Coordinates and Parameter-Topology Files
pytleap: Creating Coordinates and Parameter- Topology Files
Energy Checking Tool: ffgbsa
Energy Minimizer: minab
Molecular Dynamics "Lite": mdnab
MM(GB)(PB)/SA Analysis Tool: pymdpbsa
Appendix A: Preparing PDB Files
Appendix B: Atom and Residue Selections
Appendix C: Examples and Test Cases
sqm: Semi-empirical quantum chemistry
Available Hamiltonians
Charge-dependent exchange-dispersion corrections of vdW interactions
Dispersion and hydrogen bond correction
Usage
cpptraj
Running cpptraj
General Concepts
Data Sets and Data Files
Coordinates as a Data Set (COORDS Data Sets)
General Commands
Parameter File Commands
Trajectory File Commands
Data File Commands
Actions that Modify Topology/Coordinates
Action Commands
Matrix and Vector Actions
Data Set Analysis Commands
Coordinate Analysis Commands
Matrix and Vector Analysis
Matrix/Vector Analysis Examples
ptraj
ptraj coordinate input/output commands
ptraj commands that override the molecular information specified
ptraj action commands
Correlation and fluctuation facility
Hydrogen bonding facility
rdparm
PBSA
Introduction
Usage and keywords
Example inputs and demonstrations of functionalities
Visualization functions in pbsa
pbsa in sander and NAB
Reference Interaction Site Model
Introduction
Practical Considerations
Work Flow
rism1d
3D-RISM in NAB
rism3d.snglpnt
MMPBSA.py
Introduction
Preparing for an MM/PB(GB)SA calculation
Running MMPBSA.py
Python API
mdgx: A Developmental Molecular Simulation Engine
Input and Output
Installation
Special Algorithmic Features of mdgx
Customizable Virtual Site Support in mdgx
Restrained Electrostatic Potential Fitting in mdgx
Bonded Term Fitting in mdgx
Thermodynamic Integration
Future Directions and Goals of the mdgx Project
Miscellaneous utilities
ambpdb
reduce
elsize
Utilities for Molecular Crystal Simulations
MdoutAnalyzer.py
NAB: Introduction
Background
Methods for structure creation
Compiling nab Programs
Parallel Execution
First Examples
Molecules, Residues and Atoms
Creating Molecules
Residues and Residue Libraries
Atom Names and Atom Expressions
Looping over atoms in molecules
Points, Transformations and Frames
Creating Watson Crick duplexes
Structure Quality and Energetics
NAB: Language Reference
Introduction
Language Elements
Higher-level constructs
Statements
Structures
Functions
Points and Vectors
String Functions
Math Functions
System Functions
I/O Functions
Molecule Creation Functions
Creating Biopoloymers
Fiber Diffraction Duplexes in NAB
Reduced Representation DNA Modeling Functions
Molecule I/O Functions
Other Molecular Functions
Debugging Functions
Time and date routines
Computational resource consumption functions
NAB: Rigid-Body Transformations
Transformation Matrix Functions
Frame Functions
Functions for working with Atomic Coordinates
Symmetry Functions
Symmetry server programs
NAB: Distance Geometry
Metric Matrix Distance Geometry
Creating and manipulating bounds, embedding structures
Distance geometry templates
Bounds databases
NAB: Molecular mechanics and dynamics
Basic molecular mechanics routines
NetCDF read/write routines
Typical calling sequences
Second derivatives and normal modes
Low-MODe (LMOD) optimization methods
Using the Hierarchical Charge Partitioning (HCP) method
NAB: Sample programs
Duplex Creation Functions
nab and Distance Geometry
Building Larger Structures
Wrapping DNA Around a Path
Other examples
Bibliography
Bibliography
Index
AmberTools13Reference Manual
AmberTools13 Reference Manual
AmberTools consists of several independently developed packages that work well with Amber
itself. The main components of AmberTools are listed below.
NAB (Nucleic Acid Builder)
Thomas J. Macke, W.A. Svrcek-Seiler,
Russell A. Brown, István Kolossváry,
Yannick J. Bomble, Ramu Anandakrishnan,
David A. Case
LEaP
Wei Zhang, Tingjun Hou, Christian
Schafmeister, Wilson S. Ross, David A. Case
antechamber
Junmei Wang
amberlite
Romain M. Wolf
ptraj
Thomas E. Cheatham, III, et al. (see
http://ambermd.org/contributors.html)
cpptraj
Daniel R. Roe, et al. (see
http://ambermd.org/contributors.html)
pbsa
Jun Wang, Qin Cai, Wesley M.
Botello-Smith, Xiang Ye, Meng-Juei Hsieh,
Chuck Tan, Ray Luo
sqm
Ross C. Walker, Michael F. Crowley, Scott
Brozell, Tim Giese, Andreas W. Götz,
Tai-Sung Lee, David A. Case
CHAMBER
Michael F. Crowley, Mark Williamson, Ross
C. Walker
3D-RISM
Tyler Luchko, David A. Case, Sergey
Gusarov, Andriy Kovalenko
mdgx
David S. Cerutti
MMPBSA.py
Jason Swails, T. Dwight McGee Jr., Bill
Miller III
MTK++, MCPB
Martin Peters, Kenneth Ayers, Andrew
Wollacott, Duane E. Williams, Benjamin P.
Roberts, Kenneth M. Merz, Jr.
paramfit
Ross C. Walker, Robin Betz
1
Notes
• Most of the programs included here can be redistributed and/or modified under the terms
of the GNU General Public License; a few components have other open-source licenses.
See the amber12/AmberTools/LICENSE file for details. The programs are distributed in
the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PUR-
POSE.
• 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 "trifix" routine for random pairwise metrization is based on an algorithm designed
by Jay Ponder and was adapted from code in the Tinker package; see M.E. Hodsdon, J.W.
Ponder, and D.P. Cistola, J. Mol. Biol. 264, 585-602 (1996) and http://dasher.wustl.edu/tinker/.
• The "molsurf" routines for computing molecular surface areas were adapted from routines
written by Paul Beroza. The "sasad" routine for computing derivatives of solvent acces-
sible surface areas was kindly provided by S. Sridharan, A. Nicholls and K.A. Sharp. See
J. Computat. Chem. 8, 1038-1044 (1995).
• Some of the “pb_exmol” routines for mapping molecular surface to finite-difference grids
were adapted from routines written by Michael Gilson and Malcolm Davis in UHBD. See
Comp. Phys. Comm. 91, 57-95 (1995).
• The cifparse routines to deal with mmCIF formatted files were written by John West-
brook, and are distributed with permission. See cifparse/README for details.
Recommended Citations:
• When citing AmberTools 13 in the literature, the following citation, along with the cita-
tion of the corresponding program, 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 13, University of
California, San Francisco.
Cover Illustration
The cover shows a slice through a crystal simulation of a designed peptide; see Aravinda,
S.; Shamala, N.; Das, C.; Sriranjini, A.; Karle, I. L.; Balaram, P. J. Am. Chem. Soc., 2003,
125, 5308–15. 36 unit cells are stacked in a 4 x 3 x 3 arrangement in the triclinic super-system;
each unit cell comprises two decapeptide helices arranged roughly parallel to one another, with
water molecules forming channels perpendicular to the plane of the illustration. Figure by Dave
Cerutti.
2
Contents
Contents
1 Getting started
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Information flow in Amber .
Installation .
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1.1
1.2
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1.3 Combining AmberTools13 with Amber11 or Amber10 . . . . . . . . . . . . .
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1.4 Testing the installation .
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1.5 Applying Updates .
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1.6 Contacting the developers .
1.7 List of programs .
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2 Specifying a force field
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2.1 Specifying which force field you want in LEaP . . . . . . . . . . . . . . . . .
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2.2 The ff12SB force field .
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2.3 The AMOEBA potentials .
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2.4 The Duan et al. (2003) force field . . . . . . . . . . . . . . . . . . . . . . . .
2.5 The Yang et al. (2003) united-atom force field . . . . . . . . . . . . . . . . . .
2.6 Force fields related to semi-empirical QM . . . . . . . . . . . . . . . . . . . .
2.7 The GLYCAM force fields for carbohydrates and lipids . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . .
2.8 Lipid Force Fields .
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2.10 Solvent models .
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2.11 CHAMBER .
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2.12 Obsolete force field files
Ions .
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3 Reading and modifying Amber parameter files
3.1 Understanding Amber parameter files
3.2 ParmEd .
3.3
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paramfit
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4 LEaP
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Introduction .
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4.1
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97
4.2 Concepts
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4.3 Running LEaP .
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4.4 Basic instructions for using LEaP to build molecules
4.5 Commands
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4.6 Building oligosaccharides and lipids . . . . . . . . . . . . . . . . . . . . . . . 130
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5 Antechamber and MCPB
139
5.1 Principal programs
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5.2 A simple example for antechamber . . . . . . . . . . . . . . . . . . . . . . . . 145
5.3 Programs called by antechamber . . . . . . . . . . . . . . . . . . . . . . . . . 148
5.4 Miscellaneous programs
. . . . . . . . . . . . . . . . . . . . . . . . . 153
5.5 New Development of Antechamber And GAFF . . . . . . . . . . . . . . . . . 155
5.6 Metal Center Parameter Builder (MCPB)
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Introduction .
6 amberlite: Some AmberTools-Based Utilities
159
6.1
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6.2 Coordinates and Parameter-Topology Files . . . . . . . . . . . . . . . . . . . . 162
6.3
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pytleap: Creating Coordinates and Parameter-
Topology Files
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6.4 Energy Checking Tool: ffgbsa .
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6.5 Energy Minimizer: minab .
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6.6 Molecular Dynamics "Lite": mdnab . . . .
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6.7 MM(GB)(PB)/SA Analysis Tool: pymdpbsa . . . . .
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6.8 Appendix A: Preparing PDB Files . . . . . . . . . . . . . . . . . . . . . . . . 178
6.9 Appendix B: Atom and Residue Selections . . . . . . . . . . . . . . . . . . . . 181
6.10 Appendix C: Examples and Test Cases . . . . . . . . . . . . . . . . . . . . . . 184
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7 sqm: Semi-empirical quantum chemistry
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195
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7.1 Available Hamiltonians .
7.2 Charge-dependent exchange-dispersion corrections of vdW interactions
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7.3 Dispersion and hydrogen bond correction . . . . . . . . . . . . . . . . . . . . 198
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7.4 Usage .
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8 cpptraj
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207
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8.1 Running cpptraj .
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8.2 General Concepts .
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8.3 Data Sets and Data Files
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8.4 Coordinates as a Data Set (COORDS Data Sets) . . . . . . . . . . . . . . . . . 214
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8.6 Parameter File Commands
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8.7 Trajectory File Commands .
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8.8 Data File Commands .
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8.11 Matrix and Vector Actions
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8.12 Data Set Analysis Commands
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8.13 Coordinate Analysis Commands . . . . . . . . . . . . . . . . . . . . . . . . . 272
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8.14 Matrix and Vector Analysis .
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8.15 Matrix/Vector Analysis Examples
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4
CONTENTS
9 ptraj
283
ptraj coordinate input/output commands . . . . . . . . . . . . . . . . . . . . . 283
9.1
ptraj commands that override the molecular information specified . . . . . . . 284
9.2
ptraj action commands
9.3
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9.4 Correlation and fluctuation facility . . . . . . . . . . . . . . . . . . . . . . . . 289
9.5 Hydrogen bonding facility .
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rdparm .
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10 PBSA
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10.1 Introduction .
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10.2 Usage and keywords
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10.3 Example inputs and demonstrations of functionalities . . . . . . . . . . . . . . 314
10.4 Visualization functions in pbsa .
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10.5 pbsa in sander and NAB .
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11 Reference Interaction Site Model
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11.1 Introduction .
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11.2 Practical Considerations
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11.3 Work Flow .
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11.4 rism1d .
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11.5 3D-RISM in NAB .
11.6 rism3d.snglpnt .
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12 MMPBSA.py
349
12.1 Introduction .
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12.2 Preparing for an MM/PB(GB)SA calculation . . . . . . . . . . . . . . . . . . 350
12.3 Running MMPBSA.py .
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12.4 Python API
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13 mdgx: A Developmental Molecular Simulation Engine
377
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13.1 Input and Output
13.2 Installation .
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13.3 Special Algorithmic Features of mdgx . . . . . . . . . . . . . . . . . . . . . . 379
13.4 Customizable Virtual Site Support in mdgx . . . . . . . . . . . . . . . . . . . 380
13.5 Restrained Electrostatic Potential Fitting in mdgx . . . . . . . . . . . . . . . . 383
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13.6 Bonded Term Fitting in mdgx .
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13.7 Thermodynamic Integration .
13.8 Future Directions and Goals of the mdgx Project
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14 Miscellaneous utilities
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391
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14.1 ambpdb .
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14.2 reduce .
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14.3 elsize
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14.4 Utilities for Molecular Crystal Simulations . . . . . . . . . . . . . . . . . . . . 397
14.5 MdoutAnalyzer.py .
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5
CONTENTS
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401
15 NAB: Introduction
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15.1 Background .
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15.2 Methods for structure creation .
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15.3 Compiling nab Programs .
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15.4 Parallel Execution .
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. . . . . . . . . . . . . . . . . . . . . . . . . 408
15.5 First Examples
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. . . . . . . . . . . . . . . . . . . . . . . . . 411
15.6 Molecules, Residues and Atoms
. . . . . . . . . . . . . . . . . . . . . . . . . 412
15.7 Creating Molecules .
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. . . . . . . . . . . . . . . . . . . . . . . . . 413
15.8 Residues and Residue Libraries .
15.9 Atom Names and Atom Expressions . . . . . . . . . . . . . . . . . . . . . . . 415
15.10Looping over atoms in molecules . . . . . . . . . . . . . . . . . . . . . . . . . 417
15.11Points, Transformations and Frames . . . . . . . . . . . . . . . . . . . . . . . 418
15.12Creating Watson Crick duplexes
. . . . . . . . . . . . . . . . . . . . . . . . . 420
15.13Structure Quality and Energetics . . . . . . . . . . . . . . . . . . . . . . . . . 430
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441
16 NAB: Language Reference
. . . . . . . . . . . . . . . . . . . . . . . . . 441
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16.1 Introduction .
. . . . . . . . . . . . . . . . . . . . . . . . . 441
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16.2 Language Elements .
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. . . . . . . . . . . . . . . . . . . . . . . . . 443
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16.3 Higher-level constructs .
. . . . . . . . . . . . . . . . . . . . . . . . . 451
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16.4 Statements .
. . . . . . . . . . . . . . . . . . . . . . . . . 454
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16.5 Structures .
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16.6 Functions .
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16.7 Points and Vectors .
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16.8 String Functions .
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16.9 Math Functions .
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16.10System Functions .
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16.11I/O Functions .
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16.12Molecule Creation Functions .
. . . . . . . . . . . . . . . . . . . . . . . . . 464
16.13Creating Biopoloymers .
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16.14Fiber Diffraction Duplexes in NAB . . . . . . . . . . . . . . . . . . . . . . . . 465
16.15Reduced Representation DNA Modeling Functions . . . . . . . . . . . . . . . 466
. . . . . . . . . . . . . . . . . . . . . . . . . 466
16.16Molecule I/O Functions .
.
16.17Other Molecular Functions .
. . . . . . . . . . . . . . . . . . . . . . . . . 468
. . . . . . . . . . . . . . . . . . . . . . . . . 469
.
16.18Debugging Functions .
16.19Time and date routines
.
. . . . . . . . . . . . . . . . . . . . . . . . . 470
16.20Computational resource consumption functions . . . . . . . . . . . . . . . . . 470
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17 NAB: Rigid-Body Transformations
473
17.1 Transformation Matrix Functions . . . . . . . . . . . . . . . . . . . . . . . . . 473
17.2 Frame Functions
. . . . . . . . . . . . . . . . . . . . . . . . . 473
17.3 Functions for working with Atomic Coordinates . . . . . . . . . . . . . . . . . 474
. . . . . . . . . . . . . . . . . . . . . . . . . 474
17.4 Symmetry Functions
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17.5 Symmetry server programs .
. . . . . . . . . . . . . . . . . . . . . . . . . 477
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6
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