Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Index
A
- ACCEPTOR keyword, 27
- AKMA measurement system, 21
- ATOM keyword, 27
B
- BOND keyword, 27
C
- CHARMm
- array dimensions, 22
- data structures, 17
- force field, 11
- QUANTA mode, 12
- stand-alone mode, 12
- starting, 12
- CHARMm processes
- calculating energy, 14
- generating a PSF, 14
- generating Cartesian coordinates, 14
- performing calculations and simulations, 14
- reading model definitions, 13
- reading parameters, 13
- reading sequences, 13
- Chemistry at Harvard Macromolecular Mechanics, see CHARMm
- CLOSE command, 17
- command files
- format, 15
- title, 15
- command line, 15
- command stream
- controlling, 20
- command stream file, see command files
- commands, 15
- CLOSE, 17
- HBOND, 52
- IC BUILD, 41
- IC FILL, 41
- IC PARAMETERS, 41
- IC SEED, 41
- NBFIX, 52
- NBOND, 52
- numeric values, 16
- OPEN, 17
- options, 16
- PATCH, 36
- READ, 17
- REWIND, 44
- STREAM, 57
- WRITE, 17
- COMP keyword, 45
- conditional statements, 21
- conformations
- generating, 60, 66
- coordinate arrays
- comparison, 45
- main, 45
- coordinates
- building Cartesian, 40
- file format, 46
- generating, 39
- internal, 39
- using, 39-50
D
- diamers
- constructing, 63
- DONOR keyword, 27
E
- external files, 16
H
- harmonic restoring potential, 52
- HBOND command, 52
- hydrogen
- all-hydrogen model, 38
- constructing positions, 48
- extended atom model, 37
- modeling, 37
I
- IC BUILD command, 41
- IC FILL command, 41
- IC PARAMETERS command, 41
- IC SEED command, 41
- index number, 35
- input files, see command files
- internal coordinates, 39
- ISOP residue, 53
- IUPAC name, 33
K
- keywords, 16
- ACCEPTOR, 27
- ATOM, 27
- BOND, 27
- COMP, 45
- DONOR, 27
- PRESERVE, 41
N
- NBFIX command, 52
- NBOND command, 52
O
- OPEN command, 17
- output file, 16
P
- parameter files
- structure, 50
- using, 50-53
- parameters
- nonbonded, 52
- specifying dihedrals, 51
- specifying impropers, 51
- wildcard atom-types, 52
- PATCH command, 36
- patch residue, 35
- applying, 35
- definition, 35
- periodicity value, 52
- polyalanine helix
- constructing, 57
- polymer segments
- joining, 53
- PRESERVE keyword, 41
- protein structure file, see PSF
- PSF
- creating, 34
- modifying, 35
- structure, 33
- using, 33-37
R
- READ command, 17
- residue identifier, 33
- residue topology files, see RTF
- REWIND command, 44
- RTF, 13
- constructing and using, 25-31
- file structure, 26
- Ryckaert-Bellemans torsional potential, 53
S
- scripts
- flow control, 58
- goto statements, 58
- if statements, 58
- labels, 58
- segment identifier, 33
- .seq, 32
- sequence
- file format, 32
- using information, 32
- STREAM command, 57
V
- variables, 21
- VULC patch residue, 54
W
- WRITE command, 17
Last updated May 17, 2001.
Copyright © 2001, Accelrys Inc. All rights
reserved.