Go to the first, previous, next, last section, table of contents.

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.

#

%

*

+

-

2

=

a

ABBREV, ABBREV, ABBREV

ACCEPTOR, ACCEPTOR

ACCEPTOR Command, RTF

ACCEPTORS, ACCEPTORS, ACCEPTORS

ADD, ADD, ADD, ADD

ADD (Sphere Command)

ALAEMAX, ALAEMAX

ALL, ALL, ALL, ALL, ALL, ALL, ALL, ALL, ALL

ALLH, ALLH, ALLH

ALLSEG, ALLSEG, ALLSEG, ALLSEG

ALLTAG, ALLTAG, ALLTAG

Analysis Draw Command

Analysis END Command

Analysis READ Command

Analysis Set Command

Analysis Twist Command

Analysis WRITE Command

ANGLE, ANGLE, ANGLE, ANGLE, ANGLE, ANGLE, ANGLE

ANGLE Command, RTF

ANGLES, ANGLES, ANGLES

AS (Sphere Command)

ATOM, ATOM, ATOM, ATOM, ATOM, ATOM, ATOM, ATOM, ATOM

ATOM Command, RTF

ATOMATCH, ATOMATCH

ATOMlist (IMP PRINT Command)

ATTRIBUTE Command, RTF

AVERAGE, AVERAGE, AVERAGE, AVERAGE, AVERAGE

b

Backbone Terminal Constructions

BC (Sphere Command)

BILD Command, RTF

BOND, BOND, BOND, BOND, BOND, BOND

BOND Command, RTF

BRKHVN, BRKHVN, BRKHVN, BRKHVN

BROOKHAVEN, BROOKHAVEN, BROOKHAVEN, BROOKHAVEN

BUILD Command, RTF

BYATOM, BYATOM, BYATOM

c

C-terminus Construction

CARD, CARD, CARD, CARD

CATTRACTIVE, CATTRACTIVE

CGEN, CGEN, CGEN

CHAIN, CHAIN, CHAIN

CHARGE, CHARGE, CHARGE, CHARGE

CISTRANS, CISTRANS

CLEAR (IMP Command)

COLOR (Sphere Command)

COLUMNS, COLUMNS

COMBINATION, COMBINATION

COMP, COMP, COMP, COMP, COMP, COMP

COMPARE, COMPARE, COMPARE, COMPARE, COMPARE, COMPARE, COMPARE

COMPARE Command

CONS, CONS, CONS, CONS

CONSTRAINT, CONSTRAINT

Constraint Command

CONTACT, CONTACT

CONVergence (IMP PRINT Command)

COOR, COOR, COOR, COOR, COOR, COOR, COOR

COORDINATES, COORDINATES

COORMATCH, COORMATCH

COPY, COPY, COPY, COPY

COPY Command, RTF

COULombic (IMP PRINT Command)

CREPULSIVE, CREPULSIVE

CRS/SCP/FLCT/ATM

CS (Sphere Command)

CUT, CUT, CUT, CUT

d

DC (Sphere Command)

DECLARE Command, RTF

DEFAULT Command

DELETE, DELETE, DELETE, DELETE, DELETE, DELETE, DELETE, DELETE, DELETE, DELETE, DELETE, DELETE

DELTA, DELTA, DELTA, DELTA

DIFF, DIFF, DIFF, DIFF, DIFF, DIFF

DIHEDRAL, DIHEDRAL, DIHEDRAL

DIHEDRAL Command, RTF

DIPOle (IMP PRINT Command)

DISTANCE, DISTANCE, DISTANCE

Distance Command

DNA, DNA, DNA, DNA, DNA, DNA

DONOR Command, RTF

DONORS, DONORS, DONORS

Draw Command, Draw Command

DV (Sphere Command)

Dynamical Average Coordinate Writing

DYNAMICS, DYNAMICS

e

EACHTAG, EACHTAG

EFFEctive (IMP PRINT Command)

EIMMEDIATE, EIMMEDIATE

EINHERIT, EINHERIT

END, END, END, END

END (Sphere Command)

ENERGY, ENERGY, ENERGY, ENERGY, ENERGY, ENERGY, ENERGY, ENERGY, ENERGY, ENERGY

ENERgy (IMP PRINT Command)

EPSX, EPSX, EPSX

EPSY, EPSY, EPSY

EPSZ, EPSZ, EPSZ

Equation solving

ERINGPRO, ERINGPRO

ESURF, ESURF, ESURF

EVDW, EVDW, EVDW

EXCEPT, EXCEPT, EXCEPT, EXCEPT

EXIT (Sphere Command)

f

FILE, FILE, FILE

FIRST, FIRST, FIRST, FIRST

FIRSTU, FIRSTU, FIRSTU

FORCE, FORCE, FORCE, FORCE, FORCE, FORCE, FORCE, FORCE

g

Gaussian Command

GENERATE, GENERATE

GENERATE Command, RTF

GEOMETRY, GEOMETRY, GEOMETRY

GLOS (Sphere Command)

GLYEMAX, GLYEMAX

GRID, GRID, GRID, GRID, GRID

GROUP Command, RTF

h

HARMONIC, HARMONIC, HARMONIC

HBOND, HBOND, HBOND, HBOND, HBOND, HBOND, HBOND

HOME (Sphere Command)

HPRO, HPRO, HPRO

Hydrogen Bond Plotting

i

IGNORE, IGNORE, IGNORE, IGNORE

IMAGE (Sphere Command)

IMP CLEAR Command

IMP PRINT Command

IMP READ Command

IMP RECALL Command

IMP REMOVE Command

IMP SAVE Command

IMP SETUP Command

IMP SOLVE Command

IMP TOGRID Command

IMP VOLUME Command

IMP WRITE Command

IMPHI Command, RTF

IMPROPER, IMPROPER, IMPROPER, IMPROPER, IMPROPER

IMPROPER Command

IMPROPER Command, RTF

INITIALIZE, INITIALIZE

INTEGRATE/SQUARE

INTERIOR, INTERIOR

IR (Sphere Command)

IUPAC, IUPAC, IUPAC

j

J

JCOUPLING, JCOUPLING

k

KAPPA, KAPPA, KAPPA

KEEP, KEEP, KEEP

l

LASTRES, LASTRES

Length of Output Files

LRAN (Sphere Command)

LV (Sphere Command)

m

MAIN, MAIN, MAIN, MAIN

MANCOR, MANCOR, MANCOR

MASS, MASS, MASS, MASS, MASS, MASS

MASS Command, RTF

MAXDT, MAXDT, MAXDT, MAXDT

MAXEVDW, MAXEVDW, MAXEVDW, MAXEVDW, MAXEVDW, MAXEVDW

MAXITER, MAXITER

MERGE CG Command

MIN, MIN, MIN, MIN, MIN

MINUS (IMP PRINT Command)

n

N-terminus Construction

NAME, NAME, NAME

NBOND, NBOND, NBOND

NBXMOD, NBXMOD, NBXMOD, NBXMOD, NBXMOD, NBXMOD

NOANGLES, NOANGLES

NOAVERAGE, NOAVERAGE

NOE, NOE, NOE, NOE, NOE

NONE, NONE, NONE

NOSYMMETRY, NOSYMMETRY

NOTORSIONS, NOTORSIONS

NPRINT, NPRINT, NPRINT

NUMBER, NUMBER, NUMBER, NUMBER, NUMBER, NUMBER

NUNIT, NUNIT, NUNIT

o

OC (Sphere Command)

OD (Sphere Command)

OFFSET, OFFSET, OFFSET

OR (Sphere Command)

ORDER Command, RTF

OUTITER, OUTITER

OUTPUTU, OUTPUTU

p

Parallel Command

PARAMETER, PARAMETER, PARAMETER

PARAMETERS (IMP PRINT Command)

PARM, PARM, PARM

PBE DIFF Command

PBE DUMP Command

PBE ENERGY Command

PBE MASK Command

PBE POTENTIAL Command

PBE READ Command

PBE RECALL Command

PBE SAVE Command

PBE SETUP Command

PBE TEST Command

PBE WRITE Command

PHI, PHI, PHI, PHI, PHI, PHI, PHI

PLUS (IMP PRINT Command)

POTEntial (IMP PRINT Command)

PRINT, PRINT, PRINT, PRINT, PRINT, PRINT

PRINT (IMP Command)

PRINT Command, PRINT Command

PRINT Command, RTF

PROEMAX, PROEMAX

PROT, PROT, PROT

PSF, PSF, PSF, PSF

q

r

R

RA (Sphere Command)

RADIUS, RADIUS, RADIUS, RADIUS, RADIUS, RADIUS, RADIUS

RANDOM, RANDOM, RANDOM, RANDOM

RC (Sphere Command)

READ, READ, READ

READ (IMP Command)

READ Command in Analysis

RECALL (IMP Command)

REMOVE (IMP Command)

Reset residue color

RESID, RESID, RESID

RESIDUE, RESIDUE, RESIDUE, RESIDUE, RESIDUE, RESIDUE

RESIDUE Command, RTF

RESNAME, RESNAME, RESNAME

RESTART, RESTART

RM (Sphere Command)

RMS, RMS, RMS, RMS, RMS, RMS

RR (Sphere Command)

RS (Sphere Command)

RTF: ACCEPTOR Command

RTF: ANGLE Command

RTF: ATOM Command

RTF: ATTRIBUTE Command

RTF: BILD Command

RTF: BOND Command

RTF: BUILD Command

RTF: COPY Command

RTF: DECLARE Command

RTF: DIHEDRAL Command

RTF: DONOR Command

RTF: GENERATE Command

RTF: GROUP Command

RTF: IMPHI Command

RTF: IMPROPER Command

RTF: MASS Command

RTF: ORDER Command

RTF: PRINT Command

RTF: RESIDUE Command

RTF: SET Command

RTF: THETA Command

RTF: TORSION Command

RTF: TYPE Command

s

SA (Sphere Command)

SAVE, SAVE, SAVE, SAVE, SAVE, SAVE, SAVE, SAVE, SAVE

SAVE (IMP Command)

SCALE, SCALE, SCALE, SCALE, SCALE

SCALE (Sphere Command)

SDCO (Sphere Command)

SEED, SEED, SEED

SEQUENCE, SEQUENCE, SEQUENCE

Set Command, RTF

SETUP (IMP Command)

SFCO (Sphere Command)

SFR (Sphere Command)

SGRID, SGRID, SGRID

SHOW (Sphere Command)

SIDEOPT, SIDEOPT

SKIP, SKIP, SKIP

SL (Sphere Command)

SO (Sphere Command)

SOLVE (IMP Command)

SOLVENT, SOLVENT, SOLVENT, SOLVENT

SORT, SORT, SORT, SORT

SPECTRAL/DENSITY

Sphere Command, Sphere Command

SR (Sphere Command)

STARTRES, STARTRES, STARTRES

SURFACE, SURFACE

SYMMETRY, SYMMETRY, SYMMETRY

t

TEMPERATURE, TEMPERATURE

Terminal Residue Construction

THETA Command, RTF

TITLE, TITLE, TITLE, TITLE, TITLE, TITLE, TITLE, TITLE

TL (Sphere Command)

TLIMIT, TLIMIT, TLIMIT

TOGRID (IMP Command)

TOLERANCE, TOLERANCE, TOLERANCE

TORSION, TORSION, TORSION, TORSION

TORSION Command

TORSION Command, RTF

TORSIONS, TORSIONS, TORSIONS

TRANSFORM (Sphere Command)

TYPE, TYPE, TYPE

TYPE Command, RTF

u

UNIFORM, UNIFORM

UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT, UNIT

v

VECTOR, VECTOR, VECTOR

VOLUME (IMP Command)

w

WI (Sphere Command)

WRITDT Subroutine

WRITE, WRITE, WRITE, WRITE, WRITE

WRITE (IMP Command)

WRITE Command in Analysis

WS (Sphere Command)

x

X, X

XP (Sphere Command)

XR (Sphere Command)

XS (Sphere Command)

y

Y, Y

YP (Sphere Command)

YR (Sphere Command)

YS (Sphere Command)

z

Z, Z

ZCUT (Sphere Command)

ZMARK (Sphere Command)

ZR (Sphere Command)

Go to the first, previous, next, last section, table of contents.