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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.

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%

*

+

-

2

=

a

ACCEPTOR Command, RTF

ADD (Sphere Command)

Analysis Draw Command

Analysis END Command

Analysis READ Command

Analysis Set Command

Analysis Twist Command

Analysis WRITE Command

ANGLE Command, RTF

AS (Sphere Command)

ATOM Command, RTF

ATOMlist (IMP PRINT Command)

ATTRIBUTE Command, RTF

b

Backbone Terminal Constructions

BC (Sphere Command)

BILD Command, RTF

BOND Command, RTF

BUILD Command, RTF

c

C-terminus Construction

CLEAR (IMP Command)

COLOR (Sphere Command)

COMPARE Command

Constraint Command

CONVergence (IMP PRINT Command)

COPY Command, RTF

COULombic (IMP PRINT Command)

CRS/SCP/FLCT/ATM

CS (Sphere Command)

d

DC (Sphere Command)

DECLARE Command, RTF

DEFAULT Command

DIHEDRAL Command, RTF

DIPOle (IMP PRINT Command)

Distance Command

DONOR Command, RTF

DV (Sphere Command)

Dynamical Average Coordinate Writing

e

EFFEctive (IMP PRINT Command)

END (Sphere Command)

ENERgy (IMP PRINT Command)

Equation solving

EXIT (Sphere Command)

f

g

Gaussian Command

GENERATE Command, RTF

GLOS (Sphere Command)

GROUP Command, RTF

h

HOME (Sphere Command)

Hydrogen Bond Plotting

i

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 Command

IMPROPER Command, RTF

INTEGRATE/SQUARE

IR (Sphere Command)

j

J

k

l

Length of Output Files

LRAN (Sphere Command)

LV (Sphere Command)

m

MASS Command, RTF

MERGE CG Command

MINUS (IMP PRINT Command)

n

N-terminus Construction

o

OC (Sphere Command)

OD (Sphere Command)

OR (Sphere Command)

ORDER Command, RTF

p

Parallel Command

PARAMETERS (IMP PRINT Command)

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

PLUS (IMP PRINT Command)

POTEntial (IMP PRINT Command)

PRINT (IMP Command)

PRINT Command, RTF

q

r

R

RA (Sphere Command)

RC (Sphere Command)

READ (IMP Command)

READ Command in Analysis

RECALL (IMP Command)

REMOVE (IMP Command)

Reset residue color

RESIDUE Command, RTF

RM (Sphere Command)

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 (IMP Command)

SCALE (Sphere Command)

SDCO (Sphere Command)

Set Command, RTF

SETUP (IMP Command)

SFCO (Sphere Command)

SFR (Sphere Command)

SHOW (Sphere Command)

SL (Sphere Command)

SO (Sphere Command)

SOLVE (IMP Command)

SPECTRAL/DENSITY

SR (Sphere Command)

t

Terminal Residue Construction

THETA Command, RTF

TL (Sphere Command)

TOGRID (IMP Command)

TORSION Command

TORSION Command, RTF

TRANSFORM (Sphere Command)

TYPE Command, RTF

u

v

VOLUME (IMP Command)

w

WI (Sphere Command)

WRITDT Subroutine

WRITE (IMP Command)

WRITE Command in Analysis

WS (Sphere Command)

x

X

XP (Sphere Command)

XR (Sphere Command)

XS (Sphere Command)

y

Y

YP (Sphere Command)

YR (Sphere Command)

YS (Sphere Command)

z

Z

ZCUT (Sphere Command)

ZMARK (Sphere Command)

ZR (Sphere Command)

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