Congen V2.2.3327

CONGEN (CONformation GENerator) is a program which performs conformational searches on segments of proteins. It is most suited to problems where one needs to construct underdetermined loops or segments in a known structure, i.e. homology modeling. The program is a modification of CHARMM version 16, and has most of the capabilities of that version of CHARMM.

Congen V2.2.3327
Acknowledgements
1 Introduction to Congen
2 How to Use CONGEN
- 2.1 Controlling a CONGEN Run
- 2.2 Rules for Describing the Syntax (The Meta-Syntax)
- 2.3 Fortran I/O Units Usage by CONGEN
- 2.4 The CONGEN System of Units: AKMA.
- 2.5 Data Structures
- 2.6 Directory Names
- 2.7 Files Available for General Use
- 2.8 Size Limits
- 2.9 Sample CONGEN Runs
- 2.10 DCL or Shell CONGEN Commands
- 2.11 Interfacing to CONGEN
- 2.12 Glossary of Syntactic Terms
- 2.13 General Glossary
3 Input-Output Commands
- 3.1 READ — Reads Data from External Sources
- 3.2 WRITE — Writes Data Structures to External Files
  - 3.2.1 Syntax
  - 3.2.2 Function
- 3.3 PRINT — Writes Information to Output File (Unit 6)
  - 3.3.1 Syntax
  - 3.3.2 Function
- 3.4 Open File Command — OPEN
  - 3.4.1 Syntax
  - 3.4.2 Function
- 3.5 Close File Command — CLOSE
  - 3.5.1 Syntax
  - 3.5.2 Function
- 3.6 REWIND Command
  - 3.6.1 Syntax
  - 3.6.2 Function
- 3.7 STREAM Command
  - 3.7.1 Syntax
  - 3.7.2 Function
- 3.8 RETURN (Restore Previous Command Stream) Command
  - 3.8.1 Syntax
  - 3.8.2 Function
4 Structure Generation and Manipulation (The PSF)
- 4.1 The Generate Command - Construct a Segment of the PSF
  - 4.1.1 Syntax
  - 4.1.2 Function
- 4.2 NBXMOD — Automatic Generation of Non-bonded Exclusions
- 4.3 DISULFIDE — Creates Internal Coordinates for Disulfide Bridges
  - 4.3.1 Syntax
  - 4.3.2 Function
- 4.4 PATCH — Patches Special Structures
  - 4.4.1 Syntax
  - 4.4.2 Function
- 4.5 EDIT — Edits the PSF and Hydrogen Bonds)
5 Generation of Hydrogen Bonds
- 5.1 Syntax of the Hydrogen Bond Command
- 5.2 Purpose of the Various Hydrogen Bond Variables.
6 Generation of Non-bonded Interactions
- 6.1 Syntax for Generation of Non-bonded Interactions
- 6.2 Keywords for Generating Non-Bonded Interactions
- 6.3 Algorithms for Generating Non-bonded Interactions
- 6.4 Implementation of Non-bonded Interactions
- 6.5 Data Structures for Non-bonded Interactions
7 Minimization and Dynamics
- 7.1 Syntax for Energy Manipulation Commands
- 7.2 Requirements for Energy Manipulations
- 7.3 Energy Manipulation Options
- 7.4 Options Common to Minimization and Dynamics
- 7.5 Minimization Options
- 7.6 Running Molecular Dynamics
- 7.7 Dynamics Output
- 7.8 Manipulating Trajectories
  - 7.8.1 Merge Trajectory Syntax
  - 7.8.2 Merge Trajectory Options
8 Poisson-Boltzmann Electrostatics
- 8.1 Introduction to Poisson-Boltzmann Electrostatics
- 8.2 PBE Data Structures
- 8.3 PBE Commands
- 8.4 PBE Examples
  - 8.4.1 Calculation of the Electrostatic Binding Energy
  - 8.4.2 Poisson-Boltzmann Equation Usage in Conformational Search
9 Symmetry and Molecular Images
- 9.1 Image Files
- 9.2 Image Operation
10 Vibrational Analysis
- 10.1 Syntax for Vibrational Analysis Commands
  - 10.1.1 Main Command Syntax
  - 10.1.2 Subcommand Syntax
- 10.2 I/O For Normal modes
- 10.3 Second Derivatives
- 10.4 Normal Modes
- 10.5 Manipulation of Normal Modes
- 10.6 Exploring Energy Surfaces
11 Constraints
- 11.1 Restraining Atomic Movements
- 11.2 Holding Dihedrals Near Selected Values
- 11.3 Syntax of Dihedral Constraints
  - 11.3.1 Function of Dihedral Angle Constraints
  - 11.3.2 Other Commands
- 11.4 Fixing Atoms in Place
  - 11.4.1 Syntax for Fixing Atoms
  - 11.4.2 Function of Fixing Atoms
- 11.5 NMR Constraints
- 11.6 SHAKE — Fixing Bond Lengths Or Angles in Dynamics
- 11.7 Atom Selection
12 Conformational Search
- 12.1 Overview of Conformational Search
- 12.2 CONGEN Command Syntax
- 12.3 CONGEN Input and Output Files
- 12.4 Global Options for the CONGEN Command.
- 12.5 Degrees of Freedom
- 12.6 Examples of CONGEN Commands
- 12.7 Pointers to Relevant Programs
13 Commands to Assist in Conformational Search
- 13.1 SPLICE — Change the Sequence of the PSF.
  - 13.1.1 Syntax
  - 13.1.2 Function
- 13.2 XCONF — Extract Conformation
  - 13.2.1 Syntax
  - 13.2.2 Function
- 13.3 MERGE CG — Conformation File Manipulations
  - 13.3.1 Syntax
  - 13.3.2 Function
14 The Internal Coordinate Commands
- 14.1 Syntax of Internal Coordinates Commands
- 14.2 Purpose of the Various Internal Coordinate Commands
- 14.3 Internal Coordinate Concepts
- 14.4 Internal Coordinate File Structure
15 The Coordinate Manipulation Commands
- 15.1 Syntax of Coordinate Manipulation Commands
- 15.2 Purpose of the Coordinate Manipulation Commands
16 The Analysis Facility of CONGEN
- 16.1 An Overview of the Analysis Facility
- 16.2 Using the Analysis Facility
- 16.3 Messages and Errors
17 Table Manipulation Commands
- 17.1 Building Tables
- 17.2 Printing Tables
- 17.3 Adding Statistical Information to the Table
- 17.4 Deleting Data from Tables
18 Comparisons
- 18.1 COMPARE Command Syntax
- 18.2 The Creation of the Comparison Data Structures.
- 18.3 Matching of the Comparison Data Structures
- 18.4 Reorienting a Coordinate Trajectory
- 18.5 Comparison Messages
19 Dynamics Analysis
- 19.1 Averaging Data Structures
- 19.2 Accumulation Command — ACCUM
- 19.3 COMBINE Command — Combination of Averages
  - 19.3.1 Syntax
  - 19.3.2 Function
- 19.4 Dynamical Table Properties
  - 19.4.1 Dynamical Properties of Internal Coordinates
  - 19.4.2 Dynamical Properties of Atoms
- 19.5 Comparing Dynamics Results
20 Correlation Functions
- 20.1 Overall Syntax of the CORREL Command
- 20.2 Specification of the Trajectory Files
- 20.3 Options for the CORREL command.
- 20.4 Correlations on Normal Mode
- 20.5 Time Series Specifications
  - 20.5.1 Syntax
  - 20.5.2 Function
- 20.6 Manipulations of the Time Series and Correlation Functions
21 Reading and Writing Analysis Data
- 21.1 The Analysis READ command
  - 21.1.1 Syntax
  - 21.1.2 Function
- 21.2 The Analysis WRITE Command
  - 21.2.1 Syntax
  - 21.2.2 Function
22 Selection and Plotting Commands
- 22.1 SELECT Command — Select Data from the Table
  - 22.1.1 Syntax
  - 22.1.2 Function
- 22.2 HISTO Command — Print a Histogram
  - 22.2.1 Syntax
  - 22.2.2 Function
- 22.3 PLOT Command — Plot Data Against Position or Residue
  - 22.3.1 Syntax
  - 22.3.2 Function
- 22.4 2DPLOT Command — Make a Scatter Plot
  - 22.4.1 Syntax
  - 22.4.2 Function
23 Non-interactive Molecular Line Drawings
- 23.1 Syntax of the DRAW Command
- 23.2 Options Independent of Plotting Program
- 23.3 Operands for MOLD Drawings
- 23.4 Operands for PLT2 output.
24 Close Contact Searches
- 24.1 Close Contact Command Syntax
- 24.2 Search Command Function
25 Miscellaneous Analysis Commands
- 25.1 SET — Modify Analysis Facility Variables
  - 25.1.1 Syntax
  - 25.1.2 Function
- 25.2 TWIST — Preparing to Compute Peptide Twist
  - 25.2.1 Syntax
  - 25.2.2 Function
- 25.3 END command
  - 25.3.1 Syntax
  - 25.3.2 Function
26 Molecular Graphics
- 26.1 Sphere Drawing — CPK Style Molecular Graphics
- 26.2 PEER Command
  - 26.2.1 Syntax
  - 26.2.2 Function
27 Miscellaneous Commands
- 27.1 PARALLEL Command
  - 27.1.1 Syntax
  - 27.1.2 Function
- 27.2 CODES Command
  - 27.2.1 Syntax
  - 27.2.2 Function
- 27.3 Set Delimiter Command — DELIM
  - 27.3.1 Syntax
  - 27.3.2 Function
- 27.4 DRAW Structure Command (Obsolete)
  - 27.4.1 Syntax
  - 27.4.2 Function
- 27.5 STOP or EXIT Command
  - 27.5.1 Syntax
  - 27.5.2 Function
- 27.6 DISTANCE Command (Obsolete)
  - 27.6.1 Syntax
  - 27.6.2 Function
- 27.7 Call User Subroutine Command — USER
  - 27.7.1 Syntax
  - 27.7.2 Function
- 27.8 Set Timer Variable — TIMER
  - 27.8.1 Syntax
  - 27.8.2 Function
- 27.9 Set Warning Level Command — WRNLEV
  - 27.9.1 Syntax
  - 27.9.2 Function
- 27.10 NOBOMB Command
  - 27.10.1 Syntax
  - 27.10.2 Function
- 27.11 Set Debugging Variables — DEBUG
  - 27.11.1 Syntax
  - 27.11.2 Function
- 27.12 Set Weight Command Variables — WEIGHT
  - 27.12.1 Syntax
  - 27.12.2 Function
- 27.13 GAUSSIAN Command — Invoke Gaussian Program
  - 27.13.1 Syntax
  - 27.13.2 Function
- 27.14 TEST Command — Test Internal Functions
- 27.15 GEPOL Command — Set GEPOL Defaults
  - 27.15.1 Syntax
  - 27.15.2 Function
- 27.16 RLIMIT Command — Set Resource Limits
  - 27.16.1 Syntax
  - 27.16.2 Function
- 27.17 SHELL Command — Execute Shell Command
28 Experimental Commands
- 28.1 IMP Command
29 Support Programs
- 29.1 CONGEN Support Programs
- 29.2 Data Manipulation Commands
30 The Implementation of CONGEN
- 30.1 The Structure of CONGEN
- 30.2 Programming Environment
  - 30.2.1 Use of Fortran and FLECS
  - 30.2.2 Use of C
- 30.3 FCPP — The Fortran C Preprocessor
- 30.4 WRAPGEN — The Wrapper Generator
- 30.5 MKPROTO — Make C Function Prototypes
- 30.6 The Configuration File, config.h
- 30.7 Making CONGEN
- 30.8 Standards (Rules) for Writing CONGEN Code
- 30.9 Programming Tools
- 30.10 CONGEN Test Cases
- 30.11 Modifications to CONGEN
- 30.12 Making New Versions of CONGEN
- 30.13 Installation of CONGEN on VMS
- 30.14 Installation of CONGEN on UNIX
31 Storage Management in Fortran
- 31.1 Stacks
- 31.2 Heaps
- 31.3 Data Structures on the Heap in CONGEN
- 31.4 General Applicability of These Schemes
  - 31.4.1 Disadvantages
  - 31.4.2 Advantages
Appendix A Residue Topology Files
- A.1 Extended Atom Topology Files
- A.2 Explicit Hydrogen Topology Files
  - A.2.1 RTOPH8
- A.3 Explicit Hydrogen Topology Files
- A.4 All Hydrogen Topology Files
  - A.4.1 RTOPALLH7
- A.5 All Hydrogen Topology Files
- A.6 DNA Topology Files
Appendix B Parameter Files and Their Origins
- B.1 Development of the PARAM1 Parameter Set
- B.2 Obsolete Parameters for Proteins
- B.3 DNA Parameter Files
Command and Option Index
Concept Index

Congen V2.2.3327

Congen V2.2.3327

Table of Contents