This is the basic menu from which to operate the C-alpha
force field [Biopolymers 32, 1003-1017, 1992]. Its
organization is completely analogous to the
MAB-force field
menu. For this reason only the menu items are
listed, except where they have no corresponding item in mab.
Missing explanations can be looked up in the corresponding
items of the Section on the
MAB-force field.
The menu name mca or dca indicates whether the user has set
the dynamics toggle to energy minimization or to dynamics.
Optimizer, C-alpha Force-Field [mca,dca]
o: optimize (do force field calculation)
Energy examination and setting of constraints are two
submenus that are set up in complete analogy to
corresponding ones in the
MAB-force field
, though some of the menu
points are missing or have additional functionality as
adaption to the differences in the two force fields may
require. The user is advised to consult the on-line help for
differences.
b: submit background job
i: set number of iterations between reports
v: initialize weights
w: set weights
a: set accuracy or step size and temperature
m: set MCA mask
The force field can be run in two different modes. In
the normal one all degrees on a C-alpha of freedom are
allowed to change under the force actions. In the
restricted mode (bit 0 set) only the links (phi-psi
values) are free, while the positions remain fixed. Bit
one governs whether polar residues attract each other.
s: define stationary (fixed) residues
c: set constraints
f: forge structures
r: do rigid-body match
p: do distance positioning
e: energy examination
g: geometry examination
d: toggle minimization <-> dynamics
z: read mcc coordinates
l: write protocol item onto file
y: read in mca-file