NMRWish Built-In TCL Functions
dynEnergy: Evaluate the energy at a given step of a simulated annealing molecular structure calculation.
dynEnergy: Calculate Energy & Forces.
Restraint sources:
| Flag |
Argument |
Default |
Description |
-src |
pdbSrc |
|
Source of Structure. |
-bond |
bSrc |
|
Covalent Bonds. |
-dist |
dSrc |
|
Generic Distances. |
-angle |
aSrc |
|
Covalent Geometry Angles. |
-uangle |
uaSrc |
|
User-Supplied Angle Limits. |
-improper |
iSrc |
|
Planarity/Chirality Torsions. |
-torsion |
tSrc |
|
User-Supplied Torsion Limits. |
-j |
jSrc |
|
J-Couplings. |
-noe |
nSrc |
|
NOE Distances. |
-ds |
dsSrc |
|
Pairwise Symmetry Distances. |
-ac |
acSrc |
|
Atom Coord Constraints. |
-radGyr |
rgSrc |
|
Radius of gyration. |
-vdwex |
vdwSrc |
|
van der Waals exclusions. |
-dt |
dtSrc |
|
DELPHIC torsions. |
-dcList |
dcSrcList |
|
Dipolar Couplings for All Tensors. |
-pcs |
pcsSrc |
|
Pseudo-Contact Shifts. |
-hbond |
hbSrc |
|
Hydrogen Bonds. |
-dc |
dcSrc |
|
Dipolar Couplings. |
-dcA |
dcASrc |
|
Dipolar Couplings for Tensor A. |
-dcB |
dcBSrc |
|
Dipolar Couplings for Tensor B. |
-dcC |
dcCSrc |
|
Dipolar Couplings for Tensor C. |
Force constant scaling factors:
-bondFC |
bFC |
1.0 |
Bond Force. |
-distFC |
dFC |
1.0 |
Distance Force. |
-angleFC |
aFC |
1.0 |
Angle Force. |
-uangleFC |
aFC |
1.0 |
User Angle Force. |
-improperFC |
iFC |
1.0 |
Improper Force. |
-torsionFC |
tFC |
1.0 |
User Torsion Force. |
-jFC |
jFC |
1.0 |
J-Coupling Force. |
-noeFC |
nFC |
1.0 |
NOE Force. |
-dsFC |
dFC |
1.0 |
DS Force. |
-acFC |
aFC |
1.0 |
AC Force. |
-radGyrFC |
rFC |
1.0 |
Radius of Gyr Force. |
-radGyrSize |
rSize |
1.0 |
Radius of Gyr Size Scale. |
-hbondFC |
hFC |
1.0 |
H-Bond Force. |
-dtFC |
tFC |
1.0 |
Delphic Torsion Force. |
-dpFC |
pFC |
1.0 |
Delphic Position Force. |
-dcFC |
dFC |
1.0 |
Tensor A Dipolar Force. |
-dcAFC |
dFC |
1.0 |
Tensor A Dipolar Force. |
-dcBFC |
dFC |
1.0 |
Tensor B Dipolar Force. |
-dcCFC |
dFC |
1.0 |
Tensor C Dipolar Force. |
-csFC |
cFC |
1.0 |
Chemical Shift Force. |
-pcsFC |
pFC |
1.0 |
Pseudo-Contact Shift Force. |
-vdwFC |
vFC |
1.0 |
Van der Waals Force. |
Van der Waals Settings:
-vdwSize |
vSize |
0.0 |
VDW Radius Scale. |
-vdwMin |
vMin |
0.0 |
VDW Min Distance. |
-vdwMaxMove |
vMove |
0.5 |
Max Move in Angstroms for Recalculation of Neighborhood. |
-vdwNeighborDist |
vDist |
6.0 |
Size of Neighborhood, in Angtroms. |
Notes:
The forms -dcA -dcB etc are depricated in favor of -dcList
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