CONGEN

CONformation GENerator program

Version 2.1.2178, June 1995

Processed by TeX on @today

• Acknowledgements
• Introduction to Congen
• How to Use CONGEN
  • Controlling a CONGEN Run
  • Rules for Describing the Syntax (The Meta-Syntax)
  • Fortran I/O Units Usage by CONGEN
  • The CONGEN System of Units: AKMA.
  • Data Structures
  • Directory Names
  • Files Available for General Use
  • Size Limits
  • Sample CONGEN Runs
  • DCL or Shell CONGEN Commands
  • Interfacing to CONGEN
  • Glossary of Syntactic Terms
  • General Glossary
• Input-Output Commands
  • READ -- Reads Data from External Sources
    • Syntax of READ Command
    • Specifying a Sequence of Residues for a Segment
    • Reading coordinates
    • The Format of Parameter Files
      • Parameter File Format
      • Old Parameter File Format
    • The Format of a Residue Topology File
      • Linkage Atom Naming
      • RTF Type Command
      • RTF Mass Command
      • RTF Declare Command
      • RTF Set Command
      • RTF Order Command
      • RTF Residue Command
      • RTF Copy Command
      • RTF Attribute Command
      • RTF Atom Command
      • RTF Bond Command
      • RTF Angle Command
      • RTF Torsion Command
      • RTF Improper Command
      • RTF Donor Command
      • RTF Acceptor Command
      • RTF Build Command
      • RTF Group Command
      • RTF Generate Command
      • RTF Print Command
      • An Example RTF File
    • Reading Other Files
  • WRITE -- Writes Data Structures to External Files
    • Syntax
    • Function
  • PRINT -- Writes Information to Output File (Unit 6)
    • Syntax
    • Function
  • Open File Command -- OPEN
    • Syntax
    • Function
  • Close File Command -- CLOSE
    • Syntax
    • Function
  • REWIND Command
    • Syntax
    • Function
  • STREAM Command
    • Syntax
    • Function
  • RETURN (Restore Previous Command Stream) Command
    • Syntax
    • Function
• Structure Generation and Manipulation (The PSF)
  • The Generate Command - Construct a Segment of the PSF
    • Syntax
    • Function
  • NBXMOD -- Automatic Generation of Non-bonded Exclusions
  • DISULFIDE -- Creates Internal Coordinates for Disulfide Bridges
    • Syntax
    • Function
  • PATCH -- Patches Special Structures
    • Syntax
    • Function
  • EDIT -- Edits the PSF and Hydrogen Bonds)
    • Syntax
    • Function
    • ADD and DELETE -- Modify the Structure Arrays
      • Syntax
      • Function
    • MODIFY -- Changes the Attributes of an Atom
      • Syntax
    • Function
• Generation of Hydrogen Bonds
  • Syntax of the Hydrogen Bond Command
  • Purpose of the Various Hydrogen Bond Variables.
• Generation of Non-bonded Interactions
  • Syntax for Generation of Non-bonded Interactions
  • Keywords for Generating Non-Bonded Interactions
  • Algorithms for Generating Non-bonded Interactions
  • Implementation of Non-bonded Interactions
  • Data Structures for Non-bonded Interactions
• Minimization and Dynamics
  • Syntax for Energy Manipulation Commands
  • Requirements for Energy Manipulations
  • Energy Manipulation Options
  • Options Common to Minimization and Dynamics
  • Minimization Options
  • Running Molecular Dynamics
  • Dynamics Output
  • Manipulating Trajectories
    • Merge Trajectory Syntax
    • Merge Trajectory Options
• Poisson-Boltzmann Electrostatics
  • Introduction to Poisson-Boltzmann Electrostatics
  • PBE Data Structures
  • PBE Commands
    • PBE SETUP Command
    • PBE POTENTIAL Command
    • PBE ENERGY Command
    • PBE READ Command
    • PBE WRITE Command
    • PBE TEST Command
    • PBE SAVE Command
    • PBE RECALL Command
    • PBE DIFF Command
    • PBE DESTROY Command
    • PBE STATISTICS Command
    • PBE DUMP Command
    • PBE MASK Command
  • PBE Examples
    • Calculation of the Electrostatic Binding Energy
    • Poisson-Boltzmann Equation Usage in Conformational Search
• Symmetry and Molecular Images
  • Image Files
  • Image Operation
• Vibrational Analysis
  • Syntax for Vibrational Analysis Commands
    • Main Command Syntax
    • Subcommand Syntax
  • I/O For Normal modes
  • Second Derivatives
  • Normal Modes
  • Manipulation of Normal Modes
  • Exploring Energy Surfaces
• Constraints
  • Restraining Atomic Movements
    • Syntax of Harmonic Atom Constraints
    • Function of Harmonic Atom Constraints
    • Other Commands for Harmonic Atom Constraints
  • Holding Dihedrals Near Selected Values
  • Syntax of Dihedral Constraints
    • Function of Dihedral Angle Constraints
    • Other Commands
  • Fixing Atoms in Place
    • Syntax for Fixing Atoms
    • Function of Fixing Atoms
  • NMR Constraints
    • Theory for NOE Constraints
    • Theory for J Coupling Constraints
    • Syntax for NMR Constraint Command
    • Keywords for NMR Constraint Command
    • NMR Constraint Files
      • TYPE command
      • WEIGHT command
      • ENSEMBLE Command
      • CONS Command
      • JOIN command
      • END command
      • Examples
  • SHAKE -- Fixing Bond Lengths Or Angles in Dynamics
  • Atom Selection
    • Syntax of an Atom-Selection
    • Interpretation of Atom Selection Tokens
    • Selection Tokens
    • Operators on Selections
    • Examples of Atom Selections
• Conformational Search
  • Overview of Conformational Search
    • Overview of the Backbone and Chain Closure
    • Overview of Sidechain Degree of Freedom
    • Overview of Directed Searching
    • Parallel Processing
  • CONGEN Command Syntax
  • CONGEN Input and Output Files
    • Torsion Angle Maps
    • Proline Constructor File
    • Sidechain Topology File
      • RESIDUE command
      • CLUMP command
      • ATOM command
      • PRINT command
      • COPY command
      • END command
    • Conformations File
    • Status File
    • Checkpoint File
  • Global Options for the CONGEN Command.
    • Search Method Options
    • Conformational Search Limits
    • Maps and Construction Tables
    • Energy Calculation Options
    • Poisson-Boltzmann Options
    • Search Tree Pruning Options
    • Checkpoint and Restart Options
    • Status Display Options
    • Miscellaneous Global Options
  • Degrees of Freedom
    • Backbone Degree of Freedom
    • Chain Closure Degree of Freedom
    • Sidechain Degree of Freedom
    • Read Best Conformations Degree of Freedom
    • Write Conformations Degree of Freedom
    • Evaluate Degree of Freedom
  • Examples of CONGEN Commands
    • Five Residue Search
    • Complete Sidechain Reconstruction Example
    • Energy Directed Search Example
  • Pointers to Relevant Programs
• Commands to Assist in Conformational Search
  • SPLICE -- Change the Sequence of the PSF.
    • Syntax
    • Function
  • XCONF -- Extract Conformation
    • Syntax
    • Function
  • MERGE CG -- Conformation File Manipulations
    • Syntax
    • Function
• The Internal Coordinate Commands
  • Syntax of Internal Coordinates Commands
  • Purpose of the Various Internal Coordinate Commands
  • Internal Coordinate Concepts
  • Internal Coordinate File Structure
• The Coordinate Manipulation Commands
  • Syntax of Coordinate Manipulation Commands
  • Purpose of the Coordinate Manipulation Commands
    • The INITIALIZE command
    • The COPY command
    • The SWAP command
    • The AVERAGE command
    • The TRANSLATE command
    • The ROTATE Command
    • The ORIENT Command
    • The RMS Command
    • The RANDOM Command
    • The DIFF Command
    • The XFORM Command
    • The XINVERT Command
    • The SCALE Command
    • The CONVERT Command
    • The EQUIVALENCE Command
    • The Unit Cell Coordinate Manipulation Commands
    • HBUILD Command
• The Analysis Facility of CONGEN
  • An Overview of the Analysis Facility
  • Using the Analysis Facility
  • Messages and Errors
• Table Manipulation Commands
  • Building Tables
    • Syntax of the BUILD Command
    • Table Classes and the Selection of Tags
    • Table Properties
      • Static Properties of Internal Coordinates
      • Static Properties of Hydrogen Bonds
      • Static Properties of Atoms
    • Execution Time of the BUILD Command
    • DIFF and COMPARE Build Table Options
    • Table Input and Output
  • Printing Tables
    • Print Command Syntax
    • Pretty Table Printing
    • Multiple Column Printing
    • Print Table Options
  • Adding Statistical Information to the Table
    • Syntax of the ADD command
    • Selection of Table Statistics
    • Collection of Table Data
    • Placement of Table Statistics
  • Deleting Data from Tables
    • DELETE Command Syntax
    • Deletion from Standard Tables
      • Deletion of Segments
      • Deletion of Residues
      • Deletion of Data
      • Cleaning of the Table
    • Accommodations for Difference Tables
• Comparisons
  • COMPARE Command Syntax
  • The Creation of the Comparison Data Structures.
  • Matching of the Comparison Data Structures
  • Reorienting a Coordinate Trajectory
  • Comparison Messages
• Dynamics Analysis
  • Averaging Data Structures
  • Accumulation Command -- ACCUM
    • Syntax
    • Function
    • Files Required
    • Required Operands in the Command
    • Options
  • COMBINE Command -- Combination of Averages
    • Syntax
    • Function
  • Dynamical Table Properties
    • Dynamical Properties of Internal Coordinates
    • Dynamical Properties of Atoms
      • Dynamic Properties of Position and Velocity
      • Properties of the Anisotropy of the Motion
      • Atomic "Temperature" Properties
      • Properties of the Principal Axis of Motion
  • Comparing Dynamics Results
• Correlation Functions
  • Overall Syntax of the CORREL Command
  • Specification of the Trajectory Files
  • Options for the CORREL command.
  • Correlations on Normal Mode
  • Time Series Specifications
    • Syntax
    • Function
  • Manipulations of the Time Series and Correlation Functions
    • Manipulation Syntax
    • Making Plots of the Time Series or Correlation Functions
    • Manipulating the Time Series
    • Calculating a Correlation Function
    • Manipulating the Correlation Functions
    • Resetting Back to the Original Time Series
• Reading and Writing Analysis Data
  • The Analysis READ command
    • Syntax
    • Function
  • The Analysis WRITE Command
    • Syntax
    • Function
• Selection and Plotting Commands
  • SELECT Command -- Select Data from the Table
    • Syntax
    • Function
  • HISTO Command -- Print a Histogram
    • Syntax
    • Function
  • PLOT Command -- Plot Data Against Position or Residue
    • Syntax
    • Function
  • 2DPLOT Command -- Make a Scatter Plot
    • Syntax
    • Function
• Non-interactive Molecular Line Drawings
  • Syntax of the DRAW Command
  • Options Independent of Plotting Program
  • Operands for MOLD Drawings
  • Operands for PLT2 output.
• Close Contact Searches
  • Close Contact Command Syntax
  • Search Command Function
• Miscellaneous Analysis Commands
  • SET -- Modify Analysis Facility Variables
    • Syntax
    • Function
  • TWIST -- Preparing to Compute Peptide Twist
    • Syntax
    • Function
  • END command
    • Syntax
    • Function
• Molecular Graphics
  • Sphere Drawing -- CPK Style Molecular Graphics
    • Overview of Sphere Drawing
    • Using the Sphere Drawing Commands
    • Atom Manipulations
      • ADD -- Mark Atoms for the Spheres List
      • COLOR -- Color Atoms
      • DC -- Define Colors
      • SFR -- Set Radius for Surface Coloring
      • SFCO -- Set Color for Accessible Surface
      • RA -- Set Atom Radii
      • RC -- Reset Colors
      • RM -- Unmark (Remove) Atoms
      • RR -- Reset Atomic Radii
      • ZMARK -- Mark Atoms by the Z Coordinate
    • Transformations from the Coordinates to the Image
      • AS -- Automatic Scaling
      • DV -- Set Device Drawing Parameters
      • HOME -- Reset Sphere Drawing Parameters
      • IR -- Input Rotation Matrix
      • OC -- Shift Screen Origin in Centimeters
      • OD -- Set Origin of Data
      • OR -- Set Origin of Data in Screen Size Units
      • SA -- Scale in Angstrom Units
      • SCALE -- Scale by a Multiplicative Factor
      • SHOW, SR -- Show Drawing Parameters
      • SO -- Set Stereo Offset
      • XP -- Set Horizontal (X) Pixel Count
      • XR -- X Rotation
      • XS -- Set Horizontal (X) Screen Size
      • YP -- Set Vertical (Y) Pixel Count
      • YR -- Y Rotation
      • YS -- Set Vertical (Y) Screen Size
      • ZCUT -- Mark Atoms by Transformed Z's
      • ZR -- Z Rotation
    • Controlling Data Flow
      • CS -- Clear Spheres List
      • IMAGE -- Make the Sphere Drawing Image
      • RS -- Read Sphere List from a File
      • TL -- Set Title
      • TRANSFORM -- Transform Atoms to Spheres
      • WI -- Write Image to a File
      • WS -- Write Spheres to a File
    • Adjustment of the Lighting and Shading
      • BC -- Set Background Color
      • GLOS -- Set Glossiness Drawing Parameter
      • LRAN -- Set Lighting Range
      • LV -- Set Lighting Vector
      • SDCO -- Set Lighting Coefficients
      • SL -- Show Lighting Parameters
    • Miscellaneous Sphere Drawing Commands
      • END, EXIT -- Exit Sphere Drawing
    • Example 1 -- Full Screen Image
    • Example 2 -- Making a Stereo Image
    • Example 3 -- Nine Drawings in One Image
    • Displaying Pictures
      • diris -- Display on Iris 4D workstations
      • sphrgb -- Convert to SGI RGB Format
      • DI340 -- Display images on PS340
      • DISPIMG -- Display Images on the Deanza
      • DISPMANY -- Display Many Images on Deanza
      • SLU -- Gamma Correction for E&S PS 340
  • PEER Command
    • Syntax
    • Function
• Miscellaneous Commands
  • PARALLEL Command
    • Syntax
    • Function
  • CODES Command
    • Syntax
    • Function
  • Set Delimiter Command -- DELIM
    • Syntax
    • Function
  • DRAW Structure Command (Obsolete)
    • Syntax
    • Function
  • STOP or EXIT Command
    • Syntax
    • Function
  • DISTANCE Command (Obsolete)
    • Syntax
    • Function
  • Call User Subroutine Command -- USER
    • Syntax
    • Function
  • Set Timer Variable -- TIMER
    • Syntax
    • Function
  • Set Warning Level Command -- WRNLEV
    • Syntax
    • Function
  • NOBOMB Command
    • Syntax
    • Function
  • Set Debugging Variables -- DEBUG
    • Syntax
    • Function
  • Set Weight Command Variables -- WEIGHT
    • Syntax
    • Function
  • GAUSSIAN Command -- Invoke Gaussian Program
    • Syntax
    • Function
  • TEST Command -- Test Internal Functions
    • Test Command Syntax
    • Energy Derivative Test
    • Vavoid Hydrogen Bond Test
    • Torsion Energy Minimum Test
  • GEPOL Command -- Set GEPOL Defaults
    • Syntax
    • Function
  • RLIMIT Command -- Set Resource Limits
    • Syntax
    • Function
  • SHELL Command -- Execute Shell Command
• Experimental Commands
  • IMP Command
    • Inducible Multipole Solvation Theory
    • Syntax and Usage of the IMP command.
      • Initializing an IMPS calculation
      • Solving for the induced multipole moments
      • Print IMP parameters and results
      • Read an IMP structure from a file
      • Write an IMP structure to a file
      • Save an IMP structure by name
      • Recall a saved IMP structure
      • Remove a saved IMP structure
      • Clear the current IMP structure
      • Generate a PBE-type potential grid
      • Print atomic volumes
    • Usage Examples
      • IMPS solvation energy calculation
    • Deciphering error messages
• Support Programs
  • CONGEN Support Programs
    • cmploop -- Preliminary Analysis of CGEN Files
    • comparecg -- Compare Two Conformation Files
    • comparecmp -- Compare Two cmploop Files
    • brkchm -- Converting Brookhaven to Congen Format
    • homology -- Simple Homology Program
    • peer -- Interactive Molecular Display Program
      • Dial Usage in Peer
      • Switches for Peer
      • Mouse Buttons for Peer
      • Keyboard Usage in Peer
      • Pop-up Menu Items for Peer
    • peercg -- Convert peer Files to CONGEN Coordinates
    • emap -- Backbone Maps and Proline Constructors
    • PDM88 -- Potential Derived Multipole Program
    • PDGRID -- Potential Derived Grid Program
  • Data Manipulation Commands
    • sortn -- Sort a Text File by Numbers (Real or Integer)
    • extract -- Extract Columns of Data from a File
    • histo -- Compute a Histogram from Data in a File
    • scat -- Compute a Scatter Plot
    • numdiff -- Difference Based on Numbers
    • ndiffpost -- Numerical Difference Postprocessor
• The Implementation of CONGEN
  • The Structure of CONGEN
  • Programming Environment
    • Use of Fortran and FLECS
    • Use of C
  • FCPP -- The Fortran C Preprocessor
  • WRAPGEN -- The Wrapper Generator
  • MKPROTO -- Make C Function Prototypes
  • The Configuration File, `config.h'
  • Making CONGEN
  • Standards (Rules) for Writing CONGEN Code
  • Programming Tools
  • CONGEN Test Cases
  • Modifications to CONGEN
  • Making New Versions of CONGEN
  • Installation of CONGEN on VMS
  • Installation of CONGEN on UNIX
• Storage Management in Fortran
  • Stacks
    • Implementation of Stacks in CONGEN
    • Useful Subprograms
      • INISTK
      • ALLSTK and ALLCSTK
      • FRESTK and FRECSTK
      • FSIZEOF
      • Other Stack Functions and Variables
      • Using Storage on the Stack
    • Stack Example 1 -- Matrix Squaring
    • Stack Example 2 -- JOINWD
  • Heaps
    • Implementation of the Heap for CONGEN
    • Useful Subprograms
      • INITHP
      • ALLHP and ALLCHP
      • FREHP and FRECHP
      • Error Detection
      • PRINHP
    • Using Storage on the Heap
    • Heap Example -- Unlimited Read of a File
  • Data Structures on the Heap in CONGEN
    • Example -- The Non-bonded List Data Structure
    • Useful Subprograms
      • STRTDT and SETUPI
      • INITDT
      • ALLDT
      • FREEDT
      • USEDDT
      • RESIZE
      • READDT and WRITDT
      • DUPLDT
    • Sharing Data and ASGNDT
    • Switching to Data Structures on the Heap
  • General Applicability of These Schemes
    • Disadvantages
    • Advantages
• Residue Topology Files
  • Extended Atom Topology Files
    • RTOP8
    • RTOP7
    • RTOP6
    • RTOP5
    • RTOP3 (Unreadable)
    • RTOP1 (Unreadable)
  • Explicit Hydrogen Topology Files
    • RTOPH8
  • Explicit Hydrogen Topology Files
    • RTOPH7
    • RTOPH6
    • RTOPH5A
    • RTOPH5
    • RTOPH4
    • RTOPH2 (Unreadable)
  • All Hydrogen Topology Files
    • RTOPALLH7
  • All Hydrogen Topology Files
    • RTOPALLH6
    • RTOPALLH5
    • RTOPALLH4
    • RTOPALLH3
  • DNA Topology Files
    • RTOPDNA4
    • RTOPDNA3
    • RTOPDNA1
    • AMBERUNIRTF
    • AMBER94RTF
• Parameter Files and Their Origins
  • Development of the PARAM1 Parameter Set
    • Geometric Constants
    • Force Constants
    • Hydrogen Bonds and Non-bonded Interactions
    • Summary and Discussion
    • Table I -- N-Methyl Acetamide Vibrational Analysis
    • Table II -- n-Butane Dihedral
    • Table III -- Comparison of Force Constants
    • PARAM2 -- Modification of PARAM1 for CO and Heme
      • Bonds
      • Angles
      • Dihedrals
      • Polarizabilities Etc.
    • PARAM3
    • PARAM4
    • PARAM5
    • AMBERPARM
    • AMBER94PARM
  • Obsolete Parameters for Proteins
    • PARMEXEL
    • PARMFIX10
    • PARMFIX9
    • PARMFIX8
    • PARMFIX7
    • PARMFIX5 (Unreadable)
    • PARMFIX2 (Unreadable)
    • PARMALLH
  • DNA Parameter Files
    • PARMDNA4
    • PARMDNA3
    • PARMDNA1
• Command and Option Index
• Concept Index

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