Command and Option Index

This index contains entries for all CONGEN commands and all CONGEN keywords. If you're trying to comprehend an example input, and you don't know what an option means, this index is the place to look.

• # Prefix: Linkage Atom Naming
• # Wildcard: Interpretation of Atom Selection Tokens
• % Wildcard: Interpretation of Atom Selection Tokens
• * Wildcard: Interpretation of Atom Selection Tokens
• + Prefix: Linkage Atom Naming
• + Wildcard: Interpretation of Atom Selection Tokens
• +n Prefix: Linkage Atom Naming
• - Prefix: Linkage Atom Naming
• -n Prefix: Linkage Atom Naming
• 2DPLOT Command: 2DPlot Command
• = Prefix: Linkage Atom Naming
• A94N: Generate Command
• A94N: Read Sequence
• A94P: Generate Command
• A94P: Read Sequence
• AA: Read Coordinates
• AA: Read Sequence
• ABBREV: Read Coordinates
• ABBREV: Read Sequence
• ABNR: Minimization
• ABS: Manipulating Time Series
• ABS: Deletion from Standard Tables
• ABS: PBE MASK Command
• ABSQ: PBE SETUP Command
• ACCEPTOR: RTF Acceptor Command
• ACCEPTOR: RTF Mass Command
• ACCEPTOR Command, RTF: RTF Acceptor Command
• ACCEPTORS: Edit Command
• ACCEPTORS: Generate Command
• ACCEPTORS: RTF Generate Command
• ADD: Select Command
• ADD: Manipulating the Correlation Functions
• ADD: Manipulating Time Series
• ADD: Sidechain Topology
• ADD (Sphere Command): Atom Manipulations in Sphere Drawing
• ADD Command: Adding Table Statistics
• ADEBYE: PBE SETUP Command
• ADJUST: RTF Residue Command
• AKMASTP: Dynamics
• ALAEMAX: Maps and Construction Tables
• ALAEMAX: Backbone and Chain Closure Overview
• ALAMAP: Maps and Construction Tables
• ALAMAP: Backbone and Chain Closure Overview
• ALL: Gaussian Command
• ALL: Table Statistics
• ALL: Sidechain Overview
• ALL: Selection Tokens
• ALL: PBE WRITE Command
• ALL: Edit Command
• ALL: Generate Command
• ALL: Print Command
• ALL: RTF Generate Command
• ALLCISTRANS: Backbone Degree of Freedom
• ALLH: Generate Command
• ALLH: RTF Type Command
• ALLH: Read Sequence
• ALLHP: Debug Command
• ALLOC: Debug Command
• ALLRES: Matching of Comparison Data
• ALLRES: Deletion from Standard Tables
• ALLSEG: Matching of Comparison Data
• ALLSEG: Deletion from Standard Tables
• ALLSTK: Debug Command
• ALLTAG: Select Command
• ALLTAG: Placement of Table Statistics
• ALLTAG: Collection of Table Data
• ALPHA: PBE SETUP Command
• ALPHA: Parameter File Format
• ALTERNATE: Read Coordinates
• ANAL: Print Command
• Analysis Draw Command: Drawing
• Analysis END Command: Analysis End Command
• Analysis READ Command: Analysis Read
• Analysis Set Command: Analysis Set Command
• Analysis Twist Command: Analysis Twist Command
• Analysis WRITE Command: Analysis Write
• ANGH: Shake Command
• ANGL: Shake Command
• ANGLE: Time Series
• ANGLE: Hydrogen Bond Properties
• ANGLE: Table Classes
• ANGLE: Internal Coordinates Function
• ANGLE: RTF Angle Command
• ANGLE: Parameter File Format
• Angle Command: Parameter File Format
• ANGLE Command, RTF: RTF Angle Command
• ANGLES: Edit Command
• ANGLES: Generate Command
• ANGLES: RTF Generate Command
• APPEND: Read Coordinates
• ARITHMETIC: PBE SETUP Command
• AROUND: Selection Tokens
• AS (Sphere Command): Transformations for Sphere Drawing
• ASGEPOL: Atom Properties
• ASURF: Gepol Command
• ASURF: Analysis Set Command
• ATOM: Search Command Function
• ATOM: Time Series
• ATOM: Table Classes
• ATOM: Energy Calculation Options
• ATOM: Sidechain Topology
• ATOM: Selection Tokens
• ATOM: PBE ENERGY Command
• ATOM: Non-bonded Keywords
• ATOM: RTF Atom Command
• ATOM Command, RTF: RTF Atom Command
• ATOMATCH: Matching of Comparison Data
• ATOMlist (IMP PRINT Command): IMP PRINT
• ATTRIBUTE: RTF Attribute Command
• ATTRIBUTE Command, RTF: RTF Attribute Command
• AUTO: Sidechain Degree of Freedom
• AVE: Table Statistics
• AVECOOR: Analysis Write
• AVERAGE: Gaussian Command
• AVERAGE: Manipulating Time Series
• AVERAGE: Function of Coordinate Manipulations
• AVERAGE: NMR Constraint File
• AVERAGE: Keywords for NMR Constraint Command
• AVERAGING: PBE SETUP Command
• AVV: Analysis Write
• AVV: Analysis Read
• AVX: Analysis Write
• AVX: Analysis Read
• BACK: Matching of Comparison Data
• BACKBONE: Backbone Degree of Freedom
• BASIS: Gaussian Command
• BC (Sphere Command): Sphere Lighting
• BEGIN: Files for Correlation Functions
• BEST: Xconf Command
• bigsortn: Sortn
• BILD: Internal Coordinates Function
• BILD: RTF Build Command
• BILD Command, RTF: RTF Build Command
• BILDS: RTF Generate Command
• BOND: Time Series
• BOND: Table Classes
• BOND: Shake Command
• BOND: Fixed Atoms
• BOND: RTF Bond Command
• BOND: Parameter File Format
• BOND Command: Parameter File Format
• BOND Command, RTF: RTF Bond Command
• BONH: Shake Command
• BREADTH: Search Method Options
• BRIEF: Correlations on Normal Modes
• brkchm: Brkchm
• BRKHVN: Write Command
• BRKHVN: Read Coordinates
• BRKHVN: Read Sequence
• BROOKHAVEN: Write Command
• BROOKHAVEN: Read Coordinates
• BROOKHAVEN: Read Sequence
• BUILD: Internal Coordinates Syntax
• BUILD: RTF Build Command
• BUILD command: Building Tables
• BUILD Command, RTF: RTF Build Command
• BUILDS: RTF Generate Command
• BULK: Gepol Command
• BYATOM: Function of Coordinate Manipulations
• BYATOM: Read Sequence
• BYNUM: Selection Tokens
• BYNUM: Harmonic Dihedrals
• BYRES: Pretty Table Printing
• BYRES: Selection Tokens
• CARD: PBE WRITE Command
• CARD: Open Command
• CARD: Read Coordinates
• CARD: Read Sequence
• CARDS: Read Sequence
• CATTRACTIVE: Parameter File Format
• CAVITY: Gepol Command
• CAVITY-EPS: PBE TEST Command
• CELL: Selection Tokens
• CENTER: PBE SETUP Command
• CG: Parallel Command
• CG: Merge CG Command
• CGCONS: Debug Command
• CGEN: Debug Command
• CGEN: Miscellaneous Global Options
• CGEN: Conformational Search
• CGSD: Minimization
• CHAIN: Chain Closure
• CHAIN: Read Sequence
• CHARGE: IMP SETUP
• CHARGE: Atom Properties
• CHARGE: PBE TEST Command
• CHARGE: PBE SETUP Command
• CHARGES: Gaussian Command
• CHECKPOINT: Checkpoint and Restart Options
• CHELP: Gaussian Command
• CHELPG: Gaussian Command
• CISTRANS: Chain Closure
• CISTRANS: Backbone Degree of Freedom
• CLDH: Harmonic Dihedrals
• CLEAR: Operators on Selections
• CLEAR: Keywords for NMR Constraint Command
• CLEAR (IMP Command): IMP CLEAR
• Close Command: Close Command
• CLSA: Backbone Degree of Freedom
• CLSA: Backbone and Chain Closure Overview
• CLSCHN: Debug Command
• CLSD: Backbone Degree of Freedom
• CLSD: Backbone and Chain Closure Overview
• CLUMP: Sidechain Degree of Freedom
• CLUMP: Sidechain Topology
• cmploop: Cmploop
• CODE: 2DPlot Command
• CODE: Plot Command
• Codes Command: Codes Command
• COEF1: NMR Constraint File
• COEF2: NMR Constraint File
• COEF3: NMR Constraint File
• COLLECT: Collection of Table Data
• COLOR (Sphere Command): Atom Manipulations in Sphere Drawing
• COLUMN: Multiple Column Printing
• COLUMNS: PBE STATISTICS Command
• COLUMNS: Print Command
• COMBINATION: Sidechain Degree of Freedom
• COMBINATION: Sidechain Overview
• COMP: Function of Coordinate Manipulations
• COMP: Merge CG Command
• COMP: Write Degree of Freedom
• COMP: Print Command
• COMP: Write Command
• COMP: Read Coordinates
• COMPARE: Analysis Twist Command
• COMPARE: General Draw Options
• COMPARE: Analysis Write
• COMPARE: Analysis Read
• COMPARE: Creation of Comparison Data
• COMPARE: Deletion from Difference Tables
• COMPARE: DIFF COMPARE Table Options
• COMPARE Command: Comparisons
• comparecg: Comparecg
• comparecmp: Comparecmp
• CONGEN: Parallel Command
• CONGEN: Conformational Search
• CONJ: Minimization
• CONNECT: General Draw Options
• CONS: Creation of Comparison Data
• CONS: Energy Calculation Options
• CONS: NMR Constraint File
• CONS: Non-bonded Keywords
• CONSERVE: Matching of Comparison Data
• CONSTANT: PBE SETUP Command
• CONSTRAINT: Print Command
• CONSTRAINT: Write Command
• Constraint Command: Harmonic Atom
• CONTACT: Atom Properties
• CONTACT: Selection Tokens
• CONVergence (IMP PRINT Command): IMP PRINT
• CONVERT: Function of Coordinate Manipulations
• COOR: Analysis Write
• COOR: Matching of Comparison Data
• COOR: Creation of Comparison Data
• COOR: Coordinate Manipulations
• COOR: Miscellaneous Global Options
• COOR: Selection Tokens
• COOR: Manipulating Trajectories
• COORDINATES: Print Command
• COORDINATES: Write Command
• COORMATCH: Reorienting a Coordinate Trajectory
• COORMATCH: Matching of Comparison Data
• COPY: Creation of Comparison Data
• COPY: Function of Coordinate Manipulations
• COPY: Sidechain Topology
• COPY: RTF Copy Command
• COPY Command, RTF: RTF Copy Command
• CORE: Rlimit Command
• CORE: Debug Command
• CORFUN: Manipulating the Correlation Functions
• CORFUN: Calculating the Correlation Functions
• CORREL Command: Correlation Functions
• COS: Manipulating Time Series
• COS2: Manipulating Time Series
• COSINE: Parameter File Format
• COULombic (IMP PRINT Command): IMP PRINT
• CPU: Rlimit Command
• CRASHU: Dynamics
• CREATE: Gaussian Command
• CREPULSIVE: Parameter File Format
• CRS/SCP/ATM: Time Series
• CRS/SCP/FLCT/ATM: Time Series
• CRS/SCP/VEC: Time Series
• CS (Sphere Command): Data Flows for Drawing Spheres
• CTOFHA: HBOND Function
• CTOFHB: HBOND Function
• CTOFNB: Non-bonded Keywords
• CTONHA: HBOND Function
• CTONHB: HBOND Function
• CTONNB: Non-bonded Keywords
• CUNIT: Write Degree of Freedom
• CUT: Energy Derivative Test
• CUT: Search Command Function
• CUT: Evl Degree of Freedom
• CUT: Write Degree of Freedom
• CUTHB: HBOND Function
• CUTHBA: HBOND Function
• CUTMP: Non-bonded Keywords
• CUTNB: Non-bonded Keywords
• CUTOFF: Pretty Table Printing
• CV: PBE TEST Command
• CYCLIC: Generate Command
• D-A: Parameter File Format
• DASH: Draw Command
• DATA: Rlimit Command
• DC (Sphere Command): Atom Manipulations in Sphere Drawing
• DEBUG: Miscellaneous Global Options
• Debug Command: Debug Command
• DECLARE: RTF Declare Command
• DECLARE Command, RTF: RTF Declare Command
• DEFAULT: Parameter File Format
• DEFAULT Command: Parameter File Format
• DELETE: Gaussian Command
• DELETE: Internal Coordinates Function
• DELETE: Close Command
• DELETE: RTF Generate Command
• DELETE: RTF Build Command
• DELETE: RTF Acceptor Command
• DELETE: RTF Donor Command
• DELETE: RTF Improper Command
• DELETE: RTF Torsion Command
• DELETE: RTF Angle Command
• DELETE: RTF Bond Command
• DELETE: RTF Attribute Command
• DELETE Command: Deleting from Tables
• Delim Command: Delim Command
• DELTA: Energy Derivative Test
• DELTA: Manipulating Time Series
• DELTA: Internal Coordinates Function
• DELTA: Backbone Degree of Freedom
• DELTAI: Manipulating Time Series
• DELTAMIN: Manipulating Time Series
• DELTAN: Manipulating Time Series
• DENSITY: Time Series
• DEPTH: Search Method Options
• DERIV: Energy Derivative Test
• DESTROY: PBE DESTROY Command
• DEVAL: Search Method Options
• DFACT: Draw Command
• DH: PBE TEST Command
• DI340: DI340
• DIAG: Correlations on Normal Modes
• DIFF: DIFF COMPARE Table Options
• DIFF: Function of Coordinate Manipulations
• DIFF: PBE DIFF Command
• DIFF: Print Command
• DIFF: Write Command
• DIFF: Read Coordinates
• DIHEDRAL: Internal Coordinates Function
• DIHEDRAL: Harmonic Dihedrals
• DIHEDRAL: RTF Torsion Command
• DIHEDRAL Command, RTF: RTF Torsion Command
• DIPOLE: Gaussian Command
• DIPOle (IMP PRINT Command): IMP PRINT
• DIRECT: Calculating the Correlation Functions
• diris: Diris
• DISPIMG: DISPIMG
• DISPMANY: DISPMANY
• DISTANCE: Hydrogen Bond Properties
• DISTANCE: Internal Coordinates Function
• DISTANCE: Parameter File Format
• Distance Command: Distance Command
• DISULFIDE: Disulfide Command
• DIV: Manipulating the Correlation Functions
• DIVZERO: Debug Command
• DNA: Generate Command
• DNA: RTF Type Command
• DNA: Read Coordinates
• DNA: Read Sequence
• DONOR: RTF Donor Command
• DONOR: RTF Mass Command
• DONOR Command, RTF: RTF Donor Command
• DONORS: Edit Command
• DONORS: Generate Command
• DONORS: RTF Generate Command
• Draw Command: Draw Command
• Draw Command: Drawing
• DUMMy: Non-bonded Keywords
• DUMMY: HBOND Function
• DV (Sphere Command): Transformations for Sphere Drawing
• Dynamical Average Coordinate Writing: Analysis Write
• DYNAMICS: Reorienting a Coordinate Trajectory
• DYNAMICS: Energy Manipulation Syntax
• EACHTAG: Placement of Table Statistics
• EACHTAG: Collection of Table Data
• EB: Weight Command
• EB: Atom Properties
• EC: Weight Command
• EC: Atom Properties
• ECHO: Keywords for NMR Constraint Command
• EDGE: PBE SETUP Command
• EDIT: Internal Coordinates Function
• EDIT: Edit Command
• EDIT ADD: Edit Add/Delete
• EDIT DELETE: Edit Add/Delete
• EDIT MODIFY: Edit Modify
• EEL: Weight Command
• EFFEctive (IMP PRINT Command): IMP PRINT
• EHB: Weight Command
• EHB: Atom Properties
• EI: Weight Command
• EI: Atom Properties
• EIGNORE: Energy Calculation Options
• EIGRNG: Minimization
• EIMMEDIATE: Search Method Options
• EIMMEDIATE: Overview of Directed Searching
• EINHERIT: Search Method Options
• EINHERIT: Overview of Directed Searching
• EJCONS: Miscellaneous Global Options
• EJCP: Weight Command
• EKETEST: Dynamics
• EL14: Parameter File Format
• ELEC: Search Command Function
• ELEC: Atom Properties
• ELED: Atom Properties
• emap: Emap
• EMAX: Backbone Degree of Freedom
• EMAX: Backbone and Chain Closure Overview
• EMIN: Parameter File Format
• ENB: Weight Command
• ENB: Search Command Function
• ENB: Atom Properties
• END: Sidechain Topology
• END: Parameter File Format
• END (Sphere Command): Miscellaneous Sphere Drawing Commands
• END Command: Parameter File Format
• ENERGY: Time Series
• ENERGY: Options for Correlation Functions
• ENERGY: Atom Properties
• ENERGY: Hydrogen Bond Properties
• ENERGY: Internal Coordinate Properties
• ENERGY: Evl Degree of Freedom
• ENERGY: Sidechain Degree of Freedom
• ENERGY: Search Method Options
• ENERGY: Energy Manipulation Syntax
• ENERGY: Print Command
• ENERgy (IMP PRINT Command): IMP PRINT
• ENOE: Weight Command
• ENSEMBLE: NMR Constraint File
• ENTER: Operators on Selections
• EP: Weight Command
• EP: Atom Properties
• EPBE: Atom Properties
• EPCONS: Miscellaneous Global Options
• EPS: Non-bonded Keywords
• EPSAVE: PBE SETUP Command
• EPSPBE: Atom Properties
• EPSX: PBE MASK Command
• EPSX: PBE STATISTICS Command
• EPSX: PBE WRITE Command
• EPSY: PBE MASK Command
• EPSY: PBE STATISTICS Command
• EPSY: PBE WRITE Command
• EPSZ: PBE MASK Command
• EPSZ: PBE STATISTICS Command
• EPSZ: PBE WRITE Command
• EQ: PBE MASK Command
• Equation solving: Debug Command
• ERINGPRO: Maps and Construction Tables
• ERINGPRO: Backbone and Chain Closure Overview
• ERXN: Atom Properties
• ESOLVE: Debug Command
• ESURF: Gepol Command
• ESURF: Debug Command
• ESURF: Xconf Command
• ET: Weight Command
• ET: Atom Properties
• ETETEST: Dynamics
• EUSER: Atom Properties
• EVAL: Sidechain Degree of Freedom
• EVAL: Search Method Options
• EVDW: Search Command Function
• EVDW: Atom Properties
• EVDW: Energy Calculation Options
• EVL: Evl Degree of Freedom
• EXCEPT: Deletion from Standard Tables
• EXCEPT: Collection of Table Data
• EXEL: Non-bonded Keywords
• EXFL: Non-bonded Keywords
• EXIT (Sphere Command): Miscellaneous Sphere Drawing Commands
• Exit Command: Stop Command
• EXNQ: Non-bonded Keywords
• EXP: NMR Constraint File
• EXPAND: Read Coordinates
• EXPOSURE: PBE SETUP Command
• extract: Extract
• EXTRADII: Gaussian Command
• FACT: Function of Coordinate Manipulations
• FACTOR: Function of Coordinate Manipulations
• FB: Atom Properties
• FC: Atom Properties
• FELD: Atom Properties
• FELE: Atom Properties
• FFT: Calculating the Correlation Functions
• FHB: Atom Properties
• FI: Atom Properties
• FILE: PBE WRITE Command
• FILE: Open Command
• FILE: Read Coordinates
• FILL: Internal Coordinates Function
• FILTER: Evl Degree of Freedom
• FILTER: Write Degree of Freedom
• FINALT: Dynamics
• FIRST: Plotting Correlation Functions
• FIRST: Merge CG Command
• FIRST: Sidechain Degree of Freedom
• FIRST: Sidechain Overview
• FIRSTT: Dynamics
• FIRSTU: Options for Correlation Functions
• FIRSTU: Reorienting a Coordinate Trajectory
• FIRSTU: Manipulating Trajectories
• FIT: Gaussian Command
• FIX: Backbone Degree of Freedom
• FIX: Fixed Atoms
• FIXED: Sidechain Overview
• FLCT/ATM: Time Series
• FMAX: Keywords for NMR Constraint Command
• FNB: Atom Properties
• FORCE: Atom Properties
• FORCE: Harmonic Dihedrals
• FORCE: Harmonic Atom
• FORCE: Print Command
• FORCE: Parameter File Format
• FORMATTED: Open Command
• FORWARD: Backbone Degree of Freedom
• FP: Atom Properties
• FPE: Debug Command
• FRAC: Search Command Function
• FRAC: Print Table Options
• FRAME: Draw Command
• FREE: Parallel Command
• FREE: Sidechain Topology
• FREQ: PLT2 Options for Draw
• FROM: Print Command
• FRXN: Atom Properties
• FSIZE: Rlimit Command
• FT: Atom Properties
• FULL: Plotting Correlation Functions
• FUSER: Atom Properties
• FVDW: Atom Properties
• GANG: Parallel Command
• GAUSSIAN: PBE SETUP Command
• Gaussian Command: Gaussian Command
• GE: PBE MASK Command
• GENERATE: AMBERUNIRTF
• GENERATE: Generate Command
• GENERATE Command, RTF: RTF Generate Command
• GENIC: Debug Command
• GEOMETRY: Time Series
• GEOMETRY: Options for Correlation Functions
• GEOMETRY: Internal Coordinate Properties
• GEPOL: Debug Command
• Gepol Command: Gepol Command
• GEPOL_INCR: Gepol Command
• GLASS: PLT2 Options for Draw
• GLOS (Sphere Command): Sphere Lighting
• GLYEMAX: Maps and Construction Tables
• GLYEMAX: Backbone and Chain Closure Overview
• GLYMAP: Maps and Construction Tables
• GLYMAP: Backbone and Chain Closure Overview
• GRID: Gaussian Command
• GRID: Debug Command
• GRID: PBE TEST Command
• GRID: PBE SETUP Command
• GRIDSIG: Debug Command
• GROUP: RTF Group Command
• GROUP Command, RTF: RTF Group Command
• GT: PBE MASK Command
• GYRATION: Time Series
• H-A: Parameter File Format
• HARMONIC: Harmonic Atom
• HARMONIC: PBE SETUP Command
• HARMONIC: Parameter File Format
• HBEXCLUDE: Parameter File Format
• HBINCLUDE: Parameter File Format
• HBOND: PLT2 Options for Draw
• HBOND: Creation of Comparison Data
• HBOND: Table Classes
• HBOND: Print Command
• HBOND: Write Command
• HBOND: Parameter File Format
• HBOND Command: Parameter File Format
• HBUILD Command: HBUILD Command
• HEIGHT: PLT2 Options for Draw
• HEME: Patch Command
• HF: Gaussian Command
• histo: Histo
• HISTO Command: Histo Command
• HISTSIZE: PBE POTENTIAL Command
• HNUSE: Write Command
• HOME (Sphere Command): Transformations for Sphere Drawing
• homology: Homology
• HOMOLOGY: Matching of Comparison Data
• HORIZ: 2DPlot Command
• HPRO: Generate Command
• HPRO: RTF Type Command
• HPRO: Read Sequence
• Hydrogen Bond Plotting: PLT2 Options for Draw
• IASORS: Dynamics
• IASVEL: Dynamics
• IC: Internal Coordinates Syntax
• IC: Print Command
• IC: Write Command
• IC: Reading Other Files
• ICAV: Analysis Write
• ICAV: Analysis Read
• ICHECW: Dynamics
• IDENT: Deletion from Standard Tables
• IDREAD: Read Coordinates
• IDREAD: Read Sequence
• IEQFRQ: Dynamics
• IFILE: Read Coordinates
• IGNORE: Multiple Column Printing
• IGNORE: PBE STATISTICS Command
• IGNORE: Read Coordinates
• IHBFRQ: General Energy Operands
• IHTFRQ: Dynamics
• IMAGE (Sphere Command): Data Flows for Drawing Spheres
• IMAGES: Print Command
• IMAGES: Write Command
• IMAXP: General Energy Operands
• IMP CLEAR Command: IMP CLEAR
• IMP Command: IMP Command
• IMP PRINT Command: IMP PRINT
• IMP READ Command: IMP READ
• IMP RECALL Command: IMP RECALL
• IMP REMOVE Command: IMP REMOVE
• IMP SAVE Command: IMP SAVE
• IMP SETUP Command: IMP SETUP
• IMP SOLVE Command: IMP SOLVE
• IMP TOGRID Command: IMP TOGRID
• IMP VOLUME Command: IMP VOLUME
• IMP WRITE Command: IMP WRITE
• IMPH: Fixed Atoms
• IMPHI: RTF Improper Command
• IMPHI: Parameter File Format
• IMPHI Command, RTF: RTF Improper Command
• IMPROPER: Time Series
• IMPROPER: Table Classes
• IMPROPER: RTF Improper Command
• IMPROPER: Parameter File Format
• IMPROPER Command: Parameter File Format
• IMPROPER Command, RTF: RTF Improper Command
• IN: Merge CG Command
• INBFRQ: General Energy Operands
• INCLUDE: Search Command Function
• INDEPENDENT: Sidechain Overview
• INDIVIDUAL: Print Command
• INEXACT: Debug Command
• INIT: Gepol Command
• INITIALIZE: Function of Coordinate Manipulations
• INITIALIZE: Read Coordinates
• INSIDRES: Search Command Function
• INSIDSEG: Search Command Function
• INTEGRATE: Manipulating the Correlation Functions
• INTEGRATE/SQUARE: Manipulating the Correlation Functions
• INTERIOR: IMP SETUP
• INTERIOR: PBE SETUP Command
• INUNIT: Analysis Set Command
• INVALID: Debug Command
• INVERT: Sidechain Topology
• INVERT: RTF Copy Command
• IONSTR: PBE TEST Command
• IONSTR: PBE SETUP Command
• IPRFRQ: Dynamics
• IPRINT: General Energy Operands
• IR (Sphere Command): Transformations for Sphere Drawing
• ISCALE: Dynamics
• ISCVEL: Dynamics
• ISEED: Dynamics
• ITERATIVE: Sidechain Overview
• IUNCRD: Dynamics
• IUNREA: Dynamics
• IUNVEL: Dynamics
• IUNWRI: Dynamics
• IUPAC: PLT2 Options for Draw
• IUPAC: Table Classes
• J: NMR Constraint File
• JCOUP: Debug Command
• JCOUPLING: Keywords for NMR Constraint Command
• JCOUPLING: Print Command
• JNORMALIZE: Keywords for NMR Constraint Command
• JOIN: NMR Constraint File
• JWEIGHT: Keywords for NMR Constraint Command
• KAPPA: PBE MASK Command
• KAPPA: PBE STATISTICS Command
• KAPPA: PBE WRITE Command
• KEEP: IMP SETUP
• KEEP: Internal Coordinates Function
• KEEP: Close Command
• KJDIFF: Keywords for NMR Constraint Command
• KONN: Write Command
• KONN: Read Coordinates
• KUNIT: Dynamics
• LABEL: PLT2 Options for Draw
• LASTRES: Sidechain Degree of Freedom
• LASTRES: Backbone Degree of Freedom
• LE: PBE MASK Command
• Length of Output Files: Analysis Set Command
• LIGA: Patch Command
• LIMIT: Search Command Function
• LIMIT: Tree Pruning Options
• LINEAR: PBE POTENTIAL Command
• LINES: PBE STATISTICS Command
• LINESZ: Analysis Set Command
• LINESZ: PBE WRITE Command
• LOG: Manipulating the Correlation Functions
• LOG: Manipulating Time Series
• LOOP: Correlations on Normal Modes
• LOOPS: Parallel Command
• LOWER: NMR Constraint File
• LP: Plotting Correlation Functions
• LRAN (Sphere Command): Sphere Lighting
• LT: PBE MASK Command
• LTC: Calculating the Correlation Functions
• LV (Sphere Command): Sphere Lighting
• M3: Table Statistics
• M4: Table Statistics
• MAIN: Creation of Comparison Data
• MAIN: Merge CG Command
• MAIN: Print Command
• MAIN: Write Command
• MALLOC: Debug Command
• MANCOR: Manipulating the Correlation Functions
• MANTIME: Manipulating Time Series
• MAP: Backbone Degree of Freedom
• MARGIN: PBE SETUP Command
• MASS: Matching of Comparison Data
• MASS: Function of Coordinate Manipulations
• MASS: Harmonic Atom
• MASS: Minimization
• MASS: RTF Mass Command
• MASS Command, RTF: RTF Mass Command
• MAX: Table Statistics
• MAX: PBE STATISTICS Command
• MAX: Print Command
• MAXCONF: Write Degree of Freedom
• MAXCUT: Evl Degree of Freedom
• MAXCUT: Write Degree of Freedom
• MAXDT: Chain Closure
• MAXDT: Backbone Degree of Freedom
• MAXDT: Backbone and Chain Closure Overview
• MAXERR: Read Coordinates
• MAXEVDW: Vavoid Hydrogen Bond Test
• MAXEVDW: Read Best Degree of Freedom
• MAXEVDW: Sidechain Degree of Freedom
• MAXEVDW: Chain Closure
• MAXEVDW: Backbone Degree of Freedom
• MAXEVDW: Sidechain Overview
• MAXG: Chain Closure
• MAXIMUM: Harmonic Dihedrals
• MAXITER: IMP SOLVE
• MAXITER: IMP SETUP
• MAXITS: PBE POTENTIAL Command
• MAXLEAF: Conformational Search Limits
• MAXNODE: Conformational Search Limits
• MAXSIDEITER: Sidechain Degree of Freedom
• MEMORY: Gaussian Command
• MERGE: Gaussian Command
• MERGE CG Command: Merge CG Command
• MERGE DYN: Manipulating Trajectories
• MIN: Table Statistics
• MIN: Sidechain Degree of Freedom
• MIN: PBE STATISTICS Command
• MIN: Print Command
• MIN: Parameter File Format
• MINCUT: Evl Degree of Freedom
• MINCUT: Write Degree of Freedom
• MINDIM: Minimization
• MINI: Evl Degree of Freedom
• MINIMIZE: Energy Manipulation Syntax
• MINIMUM: Harmonic Dihedrals
• MINRADIUS: PBE SETUP Command
• MINUS (IMP PRINT Command): IMP PRINT
• MIX: Search Method Options
• MK: Gaussian Command
• mkprocns: Emap
• MODE: Time Series
• MODEL: Read Coordinates
• MODEL: Read Sequence
• MOLSURF: PBE SETUP Command
• MSGEPOL: Atom Properties
• MULT: Manipulating Time Series
• MULTIPLICITY: Parameter File Format
• NAME: PLT2 Options for Draw
• NAME: Creation of Comparison Data
• NAME: Open Command
• NBCG: Energy Calculation Options
• NBEST: Read Best Degree of Freedom
• NBOND: Creation of Comparison Data
• NBOND: Write Command
• NBOND: Parameter File Format
• NBOND Command: Parameter File Format
• NBONDS: Non-bonded Syntax
• NBXMOD: Splice Command
• NBXMOD: Edit Command
• NBXMOD: Patch Command
• NBXMOD: Nbxmod
• NBXMOD: Generate Command
• NCGCYC: Minimization
• NCOMB: Sidechain Degree of Freedom
• NCPU: Parallel Command
• ndiffpost: Ndiffpost
• NDIV: Gepol Command
• NE: PBE MASK Command
• NEFF: Atom Properties
• NEFF: Parameter File Format
• NFILE: Reorienting a Coordinate Trajectory
• NFILE: Manipulating Trajectories
• NFREQ: Minimization
• NLTC: Calculating the Correlation Functions
• NMRC Command: Syntax for NMR Constraint Command
• NOANGLES: Edit Command
• NOANGLES: Generate Command
• NOAVERAGE: NMR Constraint File
• NOAVERAGE: Keywords for NMR Constraint Command
• NOBOMB Command: NoBomb Command
• NOBULK: Gepol Command
• NODEFREQ: Checkpoint and Restart Options
• NODIELECTRIC: PBE POTENTIAL Command
• NOE: Debug Command
• NOE: NMR Constraint File
• NOE: Keywords for NMR Constraint Command
• NOE: Print Command
• NOEIMMEDIATE: Search Method Options
• NOEINHERIT: Search Method Options
• NOENERGY: Print Command
• NOEWEIGHT: Keywords for NMR Constraint Command
• NOFAIL: Old Parameter File Format
• NOFILE: Rlimit Command
• NOFLUSH: Checkpoint and Restart Options
• NOFORCE: Print Command
• NOFR: PLT2 Options for Draw
• NOHNUSE: Write Command
• NOHOMOLOGY: Matching of Comparison Data
• NOJCOUPLING: Print Command
• NOJNORMALIZE: Keywords for NMR Constraint Command
• NOMO: Draw Command
• NONBONDED: Parameter File Format
• NONE: Gaussian Command
• NONE: PBE SETUP Command
• NONE: Print Command
• NONLINEAR: PBE POTENTIAL Command
• NONOE: Print Command
• NONORM: Calculating the Correlation Functions
• NORM: Manipulating the Correlation Functions
• NORM: Manipulating Time Series
• NORMAL: Manipulating Time Series
• NORMAL: Function of Coordinate Manipulations
• NOROT: Matching of Comparison Data
• NORUN: Gaussian Command
• NOSEQUENCE: Read Coordinates
• NOSOPT: Sidechain Degree of Freedom
• NOSOPT: Miscellaneous Global Options
• NOSORT: Print Command
• NOSYMMETRY: Sidechain Degree of Freedom
• NOSYMMETRY: Parameter File Format
• NOTABLE: Print Command
• NOTITLE: Keywords for NMR Constraint Command
• NOTORSIONS: Edit Command
• NOTORSIONS: Generate Command
• NOVAVOID: Sidechain Degree of Freedom
• NOVIOLATION: Print Command
• NOWRAP: Write Command
• NPRINT: Evl Degree of Freedom
• NPRINT: Dynamics
• NPRINT: General Energy Operands
• NRAP: Minimization
• NRESET: Manipulating the Correlation Functions
• NSAVC: Reorienting a Coordinate Trajectory
• NSAVC: Dynamics
• NSAVV: Dynamics
• NSEP: Search Command Function
• NSTEP: General Energy Operands
• NTRFRQ: Dynamics
• NUMBER: 2DPlot Command
• NUMBER: Plot Command
• NUMBER: Atom Properties
• NUMBER: Hydrogen Bond Properties
• NUMBER: Internal Coordinate Properties
• NUMBER: Xconf Command
• numdiff: Numdiff
• NUNIT: Options for Correlation Functions
• NUNIT: Reorienting a Coordinate Trajectory
• NUNIT: Manipulating Trajectories
• NWARN: PBE SETUP Command
• OC (Sphere Command): Transformations for Sphere Drawing
• OD (Sphere Command): Transformations for Sphere Drawing
• OFAC: Gepol Command
• OFF: Parallel Command
• OFF: RTF Print Command
• OFF: Parameter File Format
• OFFGRID: PBE SETUP Command
• OFFSET: Print Command
• OFFSET: Write Command
• OFFSET: Read Coordinates
• OH2: Read Sequence
• OLDGRID: PBE SETUP Command
• ON: RTF Print Command
• ON: Parameter File Format
• ONE: Edit Command
• ONE: Generate Command
• ONE: RTF Generate Command
• ONLY: Matching of Comparison Data
• Open: I/O Units
• OPEN Command: Open Command
• OR: Operators on Selections
• OR (Sphere Command): Transformations for Sphere Drawing
• ORDER: RTF Order Command
• ORDER Command, RTF: RTF Order Command
• ORIENT: Function of Coordinate Manipulations
• OSC: Manipulating Time Series
• OUT: Merge CG Command
• OUTITER: IMP SOLVE
• OUTITER: IMP SETUP
• OUTOFRES: Search Command Function
• OUTOFSEG: Search Command Function
• OUTPUTU: Reorienting a Coordinate Trajectory
• OUTPUTU: Manipulating Trajectories
• OVERFLOW: Debug Command
• OVERride: Parallel Command
• P0: Calculating the Correlation Functions
• P1: Calculating the Correlation Functions
• P2: Calculating the Correlation Functions
• PAGE: Plotting Correlation Functions
• Page Length: Analysis Set Command
• PAGESZ: Analysis Set Command
• PARA: Debug Command
• Parallel Command: Parallel Command
• PARAMETER: Print Command
• PARAMETER: Write Command
• PARAMETER: Reading Other Files
• PARAMETERS (IMP PRINT Command): IMP PRINT
• PARM: Matching of Comparison Data
• PARM: Creation of Comparison Data
• PARM: Table Classes
• PATCH: Patch Command
• PAV: Analysis Write
• PAV: Analysis Read
• PAX: Analysis Write
• PAX: Analysis Read
• PBE: Debug Command
• PBE: Creation of Comparison Data
• PBE DIFF Command: PBE DIFF Command
• PBE DUMP Command: PBE DUMP Command
• PBE ENERGY Command: PBE ENERGY Command
• PBE MASK Command: PBE MASK Command
• PBE POTENTIAL Command: PBE POTENTIAL Command
• PBE READ Command: PBE READ Command
• PBE RECALL Command: PBE RECALL Command
• PBE SAVE Command: PBE SAVE Command
• PBE SETUP Command: PBE SETUP Command
• PBE TEST Command: PBE TEST Command
• PBE WRITE Command: PBE WRITE Command
• PCUT: Minimization
• PDGRID: PDGRID
• PDM: Gaussian Command
• PDM88: PDM88
• peer: Peer
• PEER: Gepol Command
• PEER Command: Peer Command
• peercg: Peercg
• PERIOD: Parameter File Format
• PHASE: Parameter File Format
• PHI: Function of Coordinate Manipulations
• PHI: NMR Constraint File
• PHI: Fixed Atoms
• PHI: PBE MASK Command
• PHI: PBE STATISTICS Command
• PHI: PBE WRITE Command
• PHI: Parameter File Format
• PHIMIN: Torsion Energy Minimum Test
• PHIS: RTF Generate Command
• PLACE: Placement of Table Statistics
• PLOT: Plotting Correlation Functions
• PLOT Command: Plot Command
• PLT2: PLT2 Options for Draw
• PLUS (IMP PRINT Command): IMP PRINT
• POINT: Search Command Function
• POINTS: PBE SETUP Command
• POLAR: Atom Properties
• POP: Gepol Command
• POTENTIAL: Gaussian Command
• POTEntial (IMP PRINT Command): IMP PRINT
• PREFIX: Gaussian Command
• PRETTY: Pretty Table Printing
• PREVIOUS: PBE SETUP Command
• PRINT: Matching of Comparison Data
• PRINT: Sidechain Topology
• PRINT: Harmonic Atom
• PRINT: Close Command
• PRINT: RTF Print Command
• PRINT: Parameter File Format
• PRINT (IMP Command): IMP PRINT
• PRINT Command: Printing Tables
• PRINT Command: Print Command
• PRINT command: Parameter File Format
• PRINT Command, RTF: RTF Print Command
• PROB: Manipulating Time Series
• PROCONS: Maps and Construction Tables
• PROEMAX: Maps and Construction Tables
• PROEMAX: Backbone and Chain Closure Overview
• PROMAP: Maps and Construction Tables
• PROMAP: Backbone and Chain Closure Overview
• PROP: Gepol Command
• PROPERTY: Pretty Table Printing
• PROT: Generate Command
• PROT: RTF Type Command
• PROT: Read Sequence
• PROTECT: Matching of Comparison Data
• PRTFRQ: Tree Pruning Options
• PRTMIN: Minimization
• PRUNIT: Analysis Set Command
• PSF: Matching of Comparison Data
• PSF: Creation of Comparison Data
• PSF: Print Command
• PSF: Write Command
• PSI: NMR Constraint File
• PURG: Fixed Atoms
• PURGE: Internal Coordinates Function
• PUSH: Gepol Command
• QMAX: Search Method Options
• QMAX: Parallel Processing
• QMIN: Search Method Options
• QMIN: Parallel Processing
• QPOS: PBE TEST Command
• R: Atom Properties
• RA (Sphere Command): Atom Manipulations in Sphere Drawing
• RADII: PLT2 Options for Draw
• RADIUS: IMP SETUP
• RADIUS: Peer Command
• RADIUS: Atom Properties
• RADIUS: PBE TEST Command
• RADIUS: PBE POTENTIAL Command
• RADIUS: PBE SETUP Command
• RADIUS: Parameter File Format
• RAMA: Selection Tokens
• RANDOM: Function of Coordinate Manipulations
• RANDOM: Evl Degree of Freedom
• RANDOM: Sidechain Degree of Freedom
• RANDOM: Search Method Options
• RANGE: Histo Command
• RANGE: Selection Tokens
• RBEST: Read Best Degree of Freedom
• RC (Sphere Command): Atom Manipulations in Sphere Drawing
• RDEPTH: Search Method Options
• READ: Table I/O
• READ: Open Command
• READ: Read Syntax
• READ (IMP Command): IMP READ
• READ Command: Read Command
• READ Command in Analysis: Analysis Read
• RECALL: PBE MASK Command
• RECALL: PBE RECALL Command
• RECALL (IMP Command): IMP RECALL
• REDUCTION: Tree Pruning Options
• REF: Write Degree of Freedom
• REF: Harmonic Atom
• REMOVE (IMP Command): IMP REMOVE
• RES: Multiple Column Printing
• RESAVE: PBE SETUP Command
• RESEQUENCE: Splice Command
• RESET: Resetting Time Series
• Reset residue color: Pop-up Menu Items for Peer
• RESI: Non-bonded Keywords
• RESID: Matching of Comparison Data
• RESID: Deletion from Standard Tables
• RESID: Multiple Column Printing
• RESIDUE: 2DPlot Command
• RESIDUE: Plot Command
• RESIDUE: Placement of Table Statistics
• RESIDUE: Sidechain Topology
• RESIDUE: RTF Residue Command
• RESIDUE: Read Sequence
• RESIDUE Command, RTF: RTF Residue Command
• RESMATCH: Matching of Comparison Data
• RESNAME: Matching of Comparison Data
• RESNAME: Deletion from Standard Tables
• RESNAME: Selection Tokens
• RESTART: Checkpoint and Restart Options
• RETURN: Draw Command
• Return Command: Return Command
• REUSE: PBE SETUP Command
• REVERSE: Backbone Degree of Freedom
• Rewind Command: Rewind Command
• RGRID: Gepol Command
• RH2O: Analysis Set Command
• RHO: PBE MASK Command
• RHO: PBE STATISTICS Command
• RHO: PBE WRITE Command
• RM (Sphere Command): Atom Manipulations in Sphere Drawing
• RMIN: Gepol Command
• RMIN: Parameter File Format
• RMS: Table Statistics
• RMS: Function of Coordinate Manipulations
• RMS: Evl Degree of Freedom
• RMS: Sidechain Degree of Freedom
• RMS: Search Method Options
• RNA: Read Coordinates
• RNA: Read Sequence
• ROTATE: Function of Coordinate Manipulations
• ROWS: Print Command
• RR (Sphere Command): Atom Manipulations in Sphere Drawing
• RS (Sphere Command): Data Flows for Drawing Spheres
• RSOL: Gepol Command
• RSQ/ATM: Time Series
• RSS: Rlimit Command
• RTF: Print Command
• RTF: Write Command
• RTF: ACCEPTOR Command: RTF Acceptor Command
• RTF: ANGLE Command: RTF Angle Command
• RTF: ATOM Command: RTF Atom Command
• RTF: ATTRIBUTE Command: RTF Attribute Command
• RTF: BILD Command: RTF Build Command
• RTF: BOND Command: RTF Bond Command
• RTF: BUILD Command: RTF Build Command
• RTF: COPY Command: RTF Copy Command
• RTF: DECLARE Command: RTF Declare Command
• RTF: DIHEDRAL Command: RTF Torsion Command
• RTF: DONOR Command: RTF Donor Command
• RTF: GENERATE Command: RTF Generate Command
• RTF: GROUP Command: RTF Group Command
• RTF: IMPHI Command: RTF Improper Command
• RTF: IMPROPER Command: RTF Improper Command
• RTF: MASS Command: RTF Mass Command
• RTF: ORDER Command: RTF Order Command
• RTF: PRINT Command: RTF Print Command
• RTF: RESIDUE Command: RTF Residue Command
• RTF: SET Command: RTF Set Command
• RTF: THETA Command: RTF Angle Command
• RTF: TORSION Command: RTF Torsion Command
• RTF: TYPE Command: RTF Type Command
• RTOLERANCE: PBE POTENTIAL Command
• RUN: Gepol Command
• SA (Sphere Command): Transformations for Sphere Drawing
• SAMPLE: Plotting Correlation Functions
• SAVE: Gaussian Command
• SAVE: Manipulating the Correlation Functions
• SAVE: Manipulating Time Series
• SAVE: Reorienting a Coordinate Trajectory
• SAVE: Matching of Comparison Data
• SAVE: Function of Coordinate Manipulations
• SAVE: Miscellaneous Global Options
• SAVE: PBE SAVE Command
• SAVE: Close Command
• SAVE (IMP Command): IMP SAVE
• SCALAR: PLT2 Options for Draw
• SCALAR: General Draw Options
• SCALE: IMP SETUP
• SCALE: PLT2 Options for Draw
• SCALE: Function of Coordinate Manipulations
• SCALE: PBE SETUP Command
• SCALE: Dynamics
• SCALE (Sphere Command): Transformations for Sphere Drawing
• SCAN: Gaussian Command
• scat: Scat
• SCF: Gaussian Command
• SCP/ATM: Time Series
• SCP/FLCT/ATM: Time Series
• SCP/VEC: Time Series
• SD: Table Statistics
• SD: Function of Coordinate Manipulations
• SD: Minimization
• SDCO (Sphere Command): Sphere Lighting
• SDEBYE: PBE SETUP Command
• SDSAVE: Tree Pruning Options
• SEARCH: Search Method Options
• Search Command: Close Contacts
• SEARCH_NEAR: Debug Command
• SEED: Function of Coordinate Manipulations
• SEED: Internal Coordinates Function
• SEED: Miscellaneous Global Options
• SEGID: Deletion from Standard Tables
• SEGID: Multiple Column Printing
• SEGMATCH: Matching of Comparison Data
• SEGMENT: Placement of Table Statistics
• SELECT: Gaussian Command
• SELECT: Sidechain Degree of Freedom
• SELECT Command: Select Command
• SEQLINK: Peer Command
• SEQUENCE: Read Coordinates
• SEQUENCE: Read Sequence
• SET: IMP SETUP
• SET: PBE SETUP Command
• Set Command, RTF: RTF Set Command
• SETPRN: Status Display Options
• SETTO: PBE MASK Command
• SETUP: Internal Coordinates Function
• SETUP (IMP Command): IMP SETUP
• SFCO (Sphere Command): Atom Manipulations in Sphere Drawing
• SFR (Sphere Command): Atom Manipulations in Sphere Drawing
• SGRID: Torsion Energy Minimum Test
• SGRID: Sidechain Degree of Freedom
• SGRID: Sidechain Overview
• Shake Command: Shake Command
• SHELL: Gaussian Command
• SHFT: Non-bonded Keywords
• SHIFT: IMP SETUP
• SHIFT: PBE SETUP Command
• SHOW (Sphere Command): Transformations for Sphere Drawing
• SIDE: Matching of Comparison Data
• SIDE: Sidechain Degree of Freedom
• SIDEOPT: Sidechain Degree of Freedom
• SIDEOPT: Sidechain Overview
• SIMDASH: PLT2 Options for Draw
• SKIP: Files for Correlation Functions
• SKIP: Reorienting a Coordinate Trajectory
• SKIP: Manipulating Trajectories
• SL (Sphere Command): Sphere Lighting
• SLOPE: Keywords for NMR Constraint Command
• SLU: SLU
• SMOOTH: PBE SETUP Command
• SO (Sphere Command): Transformations for Sphere Drawing
• SOLVE (IMP Command): IMP SOLVE
• SOLVENT: IMP SETUP
• SOLVENT: PBE TEST Command
• SOLVENT: PBE SETUP Command
• SORT: Search Command Function
• SORT: Multiple Column Printing
• SORT: Print Command
• sortn: Sortn
• SPACING: Gaussian Command
• SPECTRAL/DENSITY: Manipulating the Correlation Functions
• Sphere Command: Usage of Sphere Drawing
• Sphere Command: Sphere Drawing
• sphrgb: Sphrgb
• SPILL: PBE SETUP Command
• SPLICE Command: Splice Command
• SQRT: Manipulating Time Series
• SQUARE: Manipulating Time Series
• SR (Sphere Command): Transformations for Sphere Drawing
• ST2: Read Sequence
• STACK: Rlimit Command
• STARTRES: Sidechain Degree of Freedom
• STARTRES: Chain Closure
• STARTRES: Backbone Degree of Freedom
• STATISTICS: PBE STATISTICS Command
• STATS: Table Statistics
• STATUS: Status Display Options
• STEP: Minimization
• STEPS: Gaussian Command
• STERN: PBE SETUP Command
• STOP: Files for Correlation Functions
• Stop Command: Stop Command
• STPLIM: Minimization
• Stream Command: Stream Command
• STRICT: Minimization
• STRUCTURE: Placement of Table Statistics
• STUNIT: Maps and Construction Tables
• SUBDIVISIONS: PBE SETUP Command
• SUM: Table Statistics
• SUM: NMR Constraint File
• SUM: Keywords for NMR Constraint Command
• SURFACE: Atom Properties
• SURFACE: Selection Tokens
• SWAP: Function of Coordinate Manipulations
• SYMMETRY: Torsion Energy Minimum Test
• SYMMETRY: Sidechain Degree of Freedom
• SYMMETRY: Parameter File Format
• SYSTEM: Print Table Options
• TABLE: General Draw Options
• TABLE: Print Command
• TAG: Multiple Column Printing
• TAGS: Select Command
• TAGS: Deletion from Standard Tables
• TAGVAL: Pretty Table Printing
• TAPE: Read Sequence
• TEMINC: Dynamics
• TEMP: Time Series
• TEMPERATURE: PBE TEST Command
• TEMPERATURE: PBE SETUP Command
• TERM: Parameter File Format
• TEST: Energy Derivative Test
• Test Command: Test Command
• TFREQ: Minimization
• THET: Fixed Atoms
• THETA: RTF Angle Command
• THETA: Parameter File Format
• THETA Command, RTF: RTF Angle Command
• THETAS: RTF Generate Command
• Time Command: Time Command
• TIMEFREQ: Checkpoint and Restart Options
• TIMESTP: Dynamics
• TITLE: 2DPlot Command
• TITLE: Plot Command
• TITLE: Histo Command
• TITLE: Table I/O
• TITLE: Merge CG Command
• TITLE: Keywords for NMR Constraint Command
• TITLE: PBE WRITE Command
• Title: Read Sequence
• TL (Sphere Command): Data Flows for Drawing Spheres
• TLIMIT: Debug Command
• TLIMIT: Dynamics
• TOGRID (IMP Command): IMP TOGRID
• TOL: Dynamics
• TOLENR: Minimization
• TOLERANCE: IMP SOLVE
• TOLERANCE: IMP SETUP
• TOLERANCE: PBE POTENTIAL Command
• TOLGRD: Minimization
• TOLITR: Minimization
• TOLSTP: Minimization
• TOP: Print Command
• TOPSAVE: Tree Pruning Options
• TORSION: Time Series
• TORSION: Table Classes
• TORSION: RTF Torsion Command
• TORSION: Parameter File Format
• TORSION Command: Parameter File Format
• TORSION Command, RTF: RTF Torsion Command
• TORSIONS: Edit Command
• TORSIONS: Generate Command
• TORSIONS: RTF Generate Command
• TOTAL: Gaussian Command
• TRAN: Function of Coordinate Manipulations
• TRANSFORM (Sphere Command): Data Flows for Drawing Spheres
• TRANSLATE: Function of Coordinate Manipulations
• TREE: Debug Command
• TREE: Tree Pruning Options
• TRILINEAR: PBE SETUP Command
• TSTRUC: Dynamics
• TWINDH: Dynamics
• TWINDL: Dynamics
• TWO: Plot Command
• TWO: Histo Command
• TWO: Select Command
• TYPE: NMR Constraint File
• TYPE: PBE SETUP Command
• TYPE: RTF Type Command
• TYPE Command, RTF: RTF Type Command
• UNDER: Gaussian Command
• UNDERFLOW: Debug Command
• UNFORMATTED: Open Command
• UNIFORM: Function of Coordinate Manipulations
• UNIFORM: PBE SETUP Command
• UNIT: Gaussian Command
• UNIT: Draw Command
• UNIT: Peer Command
• UNIT: PLT2 Options for Draw
• UNIT: 2DPlot Command
• UNIT: Plot Command
• UNIT: Creation of Comparison Data
• UNIT: Xconf Command
• UNIT: Read Best Degree of Freedom
• UNIT: Checkpoint and Restart Options
• UNIT: Keywords for NMR Constraint Command
• UNIT: PBE WRITE Command
• UNIT: PBE READ Command
• UNIT: Stream Command
• UNIT: Rewind Command
• UNIT: Close Command
• UNIT: Open Command
• UNIT: Write Command
• UNIT: Read Sequence
• UNIT: Read Command
• UNKN: RTF Type Command
• UPPER: NMR Constraint File
• USER: Evl Degree of Freedom
• User Command: User Command
• USING: PBE MASK Command
• VAHB: Vavoid Hydrogen Bond Test
• VALUE: Deletion from Standard Tables
• VAVOID: Sidechain Degree of Freedom
• VAVOID: Sidechain Overview
• VDW14: Parameter File Format
• VDWO: Non-bonded Keywords
• VECTOR: PLT2 Options for Draw
• VECTOR: General Draw Options
• VECTOR: Time Series
• VEL: Manipulating Trajectories
• VELOCITY: Options for Correlation Functions
• VERBOSE: Comparison Messages
• VERTICAL: 2DPlot Command
• VIOLATION: Print Command
• VMEM: Rlimit Command
• VOLUME: PBE SETUP Command
• VOLUME (IMP Command): IMP VOLUME
• VSGEPOL: Atom Properties
• WATER: PBE SETUP Command
• WATER: Read Sequence
• WEIGHT: NMR Constraint File
• Weight Command: Weight Command
• WEIGHTING: PBE SETUP Command
• WI (Sphere Command): Data Flows for Drawing Spheres
• WMIN: Non-bonded Keywords
• WORST: Xconf Command
• WRAP: Write Command
• WRITDT Subroutine: Analysis Read
• WRITE: Creation of Comparison Data
• WRITE: Table I/O
• WRITE: Evl Degree of Freedom
• WRITE: Write Degree of Freedom
• WRITE: Open Command
• WRITE (IMP Command): IMP WRITE
• WRITE Command: Write Command
• WRITE Command in Analysis: Analysis Write
• WRMS: Sidechain Degree of Freedom
• WRMS: Search Method Options
• Wrnlev Command: Wrnlev Command
• WRNMXD: Non-bonded Keywords
• WS (Sphere Command): Data Flows for Drawing Spheres
• WSURF: Gepol Command
• X: Atom Properties
• X: PBE WRITE Command
• X1R: NMR Constraint File
• X1S: NMR Constraint File
• XCONF: Debug Command
• XCONF Command: Xconf Command
• XDIM: PBE TEST Command
• XDIM: PBE SETUP Command
• XDIR: Function of Coordinate Manipulations
• XFORM: Function of Coordinate Manipulations
• XINVERT: Function of Coordinate Manipulations
• XP (Sphere Command): Transformations for Sphere Drawing
• XR (Sphere Command): Transformations for Sphere Drawing
• XS (Sphere Command): Transformations for Sphere Drawing
• Y: Atom Properties
• Y: PBE WRITE Command
• YDIM: PBE TEST Command
• YDIM: PBE SETUP Command
• YDIR: Function of Coordinate Manipulations
• YP (Sphere Command): Transformations for Sphere Drawing
• YR (Sphere Command): Transformations for Sphere Drawing
• YS (Sphere Command): Transformations for Sphere Drawing
• Z: Atom Properties
• Z: PBE WRITE Command
• ZCUT (Sphere Command): Transformations for Sphere Drawing
• ZDIM: PBE TEST Command
• ZDIM: PBE SETUP Command
• ZDIR: Function of Coordinate Manipulations
• ZERO: PBE SETUP Command
• ZMARK (Sphere Command): Atom Manipulations in Sphere Drawing
• ZR (Sphere Command): Transformations for Sphere Drawing