Index
A
B
C
D
E
F
G
H
I
J
L
M
N
O
P
S
T
U
V
W
A
- absolute free energy
- standalone mode of Discover program 29
- Analysis module 15
- angiotensin-converting enzyme 33
- angles
- names 70
- archive command 68
- assign angle name command 70
- assign atom pair name command 72
- assign torsion name command 74
- atom overlap, setting 176
- atom pair names 72
- atoms
- fixing 12
- restraining 25
B
- backbone, restraining 13
- begin command 78
- binff utility 21, 195
- bond order 9
- butcaptopril 34
C
- calculate absolute command 82
- calculate relative command 84
- calculations
- batch 14
- controlling 25, 30
- fine tuning 175
- interactive 14
- setting up 25
- speed 12
- stages 24
- types 1, 26
- captopril 33
- Cartesian coordinates 29
- CDiscover program compared with FDiscover program 4
- charges
- assigning 9
- chirality
- restraints 93, 95
- commands
- documentation format 6
- entering on command line in Insight program 6
- standalone 57
- comparison list generation command 89
- computation
- costs 12
- time 100, 102
- conformational changes
- controlling 13
- conformational searching 13, 14, 105
- conjugate gradient, selecting method 176
- consensus dynamics 33
- consensus dynamics/minimization 26
- constrain command 93
- Constraint pulldown 8
- constraints
- and restraints 12
- Coulombic
- interactions 11, 13, 108
- cross terms 11, 109
- importance of 11
- problems with 11
- unfound 80
- cutoff distance 14
- cutoffs 26
- CVFF 27
D
- define average atom command 96
- dielectric constant 14, 26
- distance-dependent 14
- setting 8
- dihedral restraints
- 3J 95
- dirtoseq utility 68, 196, 197
- Discover program, overview 3
- Discover Simulation Language, see DSL
- distance constraints 8
- distorted structures 11, 27, 152
- DSL
- arithmetic expressions 59, 60
- arithmetic statements 30, 58
- asterisks at start of a line, meaning of 66
- bold type in command descriptions, meaning of 66
- brackets in command descriptions, meaning of 66
- case sensitivity 21, 58
- commands 23, 58
- commands, documentation of 65
- comment statement 63
- continuation lines 64
- control, statements 60
- debugging 64
- default values 59
- end 64
- errors, checking 64
- expressions, conditional 60
- flow control 30
- format statement 63
- goto 62
- hash symbol in command descriptions, meaning of 66
- if 60
- integers 59
- italics in command descriptions, meaning of 66
- junk words 65
- keywords, list of, explanation of 67
- logical expressions 60
- loops 59
- nonstandard formats 65
- operators, comparison 60
- options, documentation of 66
- parameters, internal control 59
- print statement 63
- print using statement 62
- statements, types of 57
- syntax 58
- syntax checking 64
- then 60
- unconditional goto statement 62
- variable assignment 59, 78
- variables 30, 58
- variables controlling if statements 61
- dynamics 27
- constant-energy, constant-volume ensemble 109
- constant-pressure 14
- constant-temperature 14
- constant-temperature, constant-pressure ensemble 109
- constant-temperature, constant-volume ensemble 109
- data-collecting stage 11
- ensembles 28, 141
- equilibration 11
- example 32
- initialization 11
- parameters 177
- pressure 14
- restarting 133
- results 15
- resume phase 11
- setting up 12
- standalone mode of Discover program 28
- uses 2
E
- electric field parameters 183
- enclose command 98
- enclosure analysis 98
- energy
- maps 13
- ensembles
- see also dynamics
- ethane 32, 35
F
- files
- absolute free energy 193
- absolute free energy comparison list 193
- amber.frc 21
- .arc 23
- archive 23, 68, 196
- automatic parameter assignment 189
- .bin 21
- .car 19, 21
- Cartesian coordinate 19, 21
- cff91.frc 21
- .cli 193
- command 19, 20, 186
- constraint information 93
- controlling through Insight program 8
- coordinate 23, 25
- .cor 23
- .csh 17, 22, 79
- cvff.frc 21
- forcefield 195
- formats 4, 185
- .frc 21
- free energy scratch 193
- .frq 191
- .gre 190
- .grp 191
- .his 23
- history 15, 23, 196
- .inp 19, 20, 44, 175, 186
- input 4, 19, 185
- internal coordinate eigenvectors 191
- .log 22
- log 189
- .mdf 19, 21
- molecular data 19, 21, 25
- molecular template 187
- names 80
- .nmo 191
- optional output 24
- .ors 134, 188
- .out 22, 187
- output 22, 23, 185, 187
- .pek 22, 189
- .pre 191
- .prm 189
- .ref 116, 189
- relative free energy 192, 194
- restart 79, 134, 188, 189
- .rst 188
- scratch 191
- tabular output 190, 191
- .tbl 194
- .tem 26, 187
- template 26
- .tor 190
- torsion 190, 196
- .tot 192
- transfer between machines 196
- vibrational information 191
- warped parameters 192
- writing 44
- .wrp 192
- .xxx 193
- fix command 100
- fixed atom list generation command 102
- force command 105
- forcefields
- AMBER 14
- choosing 21
- CVFF 11
- default 21, 27
- parameters controlling 179
- specifying 25
- formhis utility 196
G
- Graph pulldown 15
- graphs 15
H
- help, on-line 5
- hydrogens
- adding 9
I
- initialize command 108
- interaction command 113
- intermolecular interaction command 116
- internal Discover parameters 175
J
- job
- checking progress 22
- controlling through Insight program 8
- number 22
- status 22
L
- log command 116
M
- magainin peptide 34
- methane 35
- methanol 32, 36
- minimization 27
- algorithms 10
- convergence 10
- default in the Discove> program 10
- definition 27
- example 31
- parameters 176
- setting up 10
- small molecules 27
- standalone mode of Discover program 27
- uses 1
- minimize command 117
- minimizers
- Broyden-Fletcher-Goldfarb-Shanno 27
- choice 8, 10, 27
- conjugate gradients 27
- default 27
- Newton-Raphson 27
- steepest descents 27
- miscellaneous parameters, setting 179, 181
- Modify pulldown 9
- molecular dynamics, see dynamics
- Morse potential 11
- movement limit, setting 176
N
- NMR data 95
- nonbond energy cutoff parameters, setting 179
- nonbond interactions 13, 14
- nuclear Overhauser effect 12, 26
O
- out-of-plane
- angle, restraining 95
- oxocaptopril 33
P
- parallel running of FDiscover 183
- Parameters pulldown 8
- peptides 34
- periodic boundary conditions 26
- parameters 182
- phenol 31
- Potentials Forcefield 9
- precision of line minimization, setting 176
- preparing models for simulation 9
- pressure control, setting parameters 178
- print command 22, 121
- prochirality restraints 95
- proteins 34
- Pseudo_Atom pulldown 8, 32
- pseudoatoms 96
- defining 8
- pull command 129
R
- random seed, setting 178
- randomize coordinates command 131
- read command 132
- reduce output command 133
- relative free energy 173
- computational requirements 32
- example 32
- running a job 46
- setting up 40
- standalone version of Discover program 29
- warped atoms 37
- residue names 21
- restart dynamics command 133, 140
- restrain command 137
- restraints
- parameters 182
- results
- analyzing 14, 29
- printing 29
- viewing in Insight program 8
- resume dynamics command 133, 140
- retrieve command 147
- rms command 148
- rotational barriers
- exploring 13
- rotors command 150
- Run pulldown 8
- Run Run 9
S
- SA446 33
- scale command 152
- Scale_Terms Parameters 14
- seqtodir utility 196
- set command 153
- Set Parameters 13
- setting up and starting an FDiscover program run 8
- simulated annealing 14
- standalone mode of Discover program
- methodology 24
- starting Discover program 4, 7, 17
- superimposition 89
- systems
- size 26
T
- tabulate command 163
- temperature 8
- control 14
- target 11
- temperature control, setting parameters 177
- template force command 165
- template forcing 8, 25, 89
- dynamic 26
- template forcing parameters 180
- template molecules 13
- tethered atom list command 168
- tethering 8, 13, 165
- torsions
- defining 8
- forcing 105
- names 21, 74
U
- uformhis utility 196, 197
V
- valences, undefined 9
- van der Waals
- interactions 13
- Variables Parameters 14
- vibrational command 28, 171
W
- warp command 173
- Warp Constraint 13
Index
Last updated September 27, 1997 at 11:17AM PDT.
Copyright © 1997, Molecular Simulations, Inc. All rights
reserved.