This is the basic menu from which to operate the force
field MAB [see J.Comp.Aided Design 9, 251-268 (1994)]. It is
a tool in the sense that it occurs in several places, but its
action may also be considered a separate modelling activity.
Whenever a energy calculation is needed the user is dropped
into this menu as the last step before the actual
calculation.
The energy calculation is performed on all active entries,
lumped together in a single molecular aggregate. Visible
entries are not affected. A couple of tools, valuable in
docking procedures, are also included here for convenience.
Most of them are also available in other menus.
The menu name mab or dab indicates whether the user has set
the dynamics toggle to energy minimization or to dynamics.
For energy calculations the number of H atoms attached to a
heavy atom must be correctly given. Otherwise incorrect
bonding situations are taken. In most cases calculations are
done with the hydrogens lumped together with their heavy
atoms (united atom approach), but the possibility exists to
take some or all of them explicitly. In any case the count of
H's (explicit and silent ones) must be correct. The present
menu serves to modify the number of silent ones. At each atom
the current number is indicated. It can be increased by
picking the atom with the left mouse button. Decrease (not
below zero) is achieved by middle button picks. No checks for
unreasonable settings are made. Some file formats have no
means to keep this information (e.g. .pdb for HETATMs). When
reading such files, usually a routine is invoked, which
generates the H-counts from geometrical criteria. In case of
poor geometry or unusual chemistry a manual modification may
be needed. This option can only be entered with active
entries.
Fully paired up electrons are always assumed. Total H-
counts that would yield a radical for net charge zero are
interpreted as a charged molecule with paired up electrons.
The energy contributions are graphically displayed.
Locations in the structures where large energy contributions
are found are colored according to a user definable energy
scale.
This menu is used to define constraints of various types in
order to influence the course of a energy minimization
calculation. Such constraints are useful in various
situations such as e.g. flexible matching, docking, etc.
When the batch option is chosen, the user is asked whether
he wants to run a sequence of force-field actions given by a
protocol. If yes, he is requested to give the name of the
protocol file to be applied. This name is written into the
control line (Cntl) of the .mab file. The batch job is then
guided by this file.
A protocol file is a sequence of lines, each of which
determines the action of the force field for the indicated
number of steps.
A new protocol instruction is indicated by the keyword
Cntl (case is important!). It can be followed by an optional
line with the keyword wgts. Both of these lines are also
automatically added to a .mab file, whenever a batch job is
issued. Thus, an easy way to generate samples of these lines
is to start issuing a batch job from Moloc, without
submitting it (option q in queue selection).
The control line is read with the following convention:
Cntl idn iter mrep acc stp tmp masf mask fnam(optional)
examples:
Cntl 0 100 0 0.100 1.000 0.5953 3 0
Cntl 1 100 30 0.100 0.500 0.7955 0 0
The parameters have the following meaning (which may be
different for minimization and dynamics runs):
wgts MABmask weights
example:
wgts 768 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
-99.9 -99.9
Cntl 1 1000 -1 0.100 0.500 0.7955 0 0
Cntl 0 0 0 0.100 0.500 0.7955 0 0
Cntl 1 1000 -1 0.100 0.500 0.7955 0 0
Cntl 0 0 0 0.100 0.500 0.7955 0 0
Cntl 1 1000 -1 0.100 0.500 0.7955 0 0
Cntl 0 0 0 0.100 0.500 0.7955 0 0
Optimizer, All-Atom Force-Field [mab,dab]
o: optimize (do force field calculation)
An interactive energy minimization is started here. It
can be interrupted at any time by hitting the escape
key. In this case the program returns to the present
menu after the current iteration is finished. The whole
setup for the energy calculation is kept to assure
immediate continuation. However, when specifications
are modified, a new setup is usually necessary.
b: submit background job
Submits a batch process with the current setup of
active entries, constraints and fixed atoms. A file
(.mab) is written which contains the necessary informa
tion. To start minimization a program called Mabch must
be found in the path. During its execution this program
writes a coordinate file (.mac) from time to time, if
iteration and repetition parameters are properly set.
For minimizations the last file is overwritten, while
for dynamics runs a trajectory is accumulated.
i: set number of iterations between reports
By default a screen update takes place after every
iteration. On slowly drawing terminals it may be advis
able to update the screen only after several itera
tions. In this option this number can be set. A printout
of the energy is only given after a minimal time of sev
eral seconds. For batch runs this parameter determines
the update rate of the resulting structure file. In the
case of a dynamics run the parameter determines the
number of time steps after which the trajectory file is
augmented by a new frame. In addition the user is asked
to specify the number of repetitions (i.e. written
frames) after which the run should stop. A value of zero
causes the program to continue indefinitely.
v: initialize weights
If the weights of the various energy terms have been
modified, they can be reset here to get the proper total
energy.
w: set weights
The various energy contributions can be independently
weighted. This is a useful tool e.g. to speed up forming
the proper hydrogen-bond pattern. However, meaningful
energies require a final relaxation with properly reset
weights. For constraints a weight of 1.0 corresponds to
the following energy amplitudes: Positional con
straints: 6, Distance constraints: 6, Torsional con
straints: 0.00914, Pyramidal constraints: 50.
a: set accuracy or step size and temperature
For minimizations a relative accuracy criterion for the
termination of the procedure can be set. For dynamics
runs this option sets a relative step size and the tem
perature.
m: set MAB mask
Several flags can be set to influence the course of the
energy calculation. They concern conservation of stere
ochemistry, H-bond pattern evaluation, and choice of
reference values. Upon leaving this option a value for
the mask is printed which corresponds to the current
choice. If this value is put into the .Moloc file, it
will be taken as default value.
s: define stationary (fixed) atoms
Upon choosing this point, the set tool is activated to
define a set of atoms which enter the energy calcula
tion with fixed positions. Only the coordinates of
atoms not contained in this set are free to change.
c: set constraints
Various types of constraints can be set to influence
the course of an energy minimization.
h: check H-atom counts
f: forge structures
r: do rigid-body match
When this option is chosen the zero-distance con
straints between atoms of active and of visible entries
are minimized by repositioning the active entries by a
common transformation.
p: do distance positioning
Here, distance constraints between atoms of active and
of visible entries are optimized by repositioning the
active entries by a common transformation. Since this
is a multiple minima problem, different results may be
obtained for different initial conditions. It may be
necessary to hit the option several times to arrive at a
final answer.
e: energy examination (new menu)
A variety of tools are provided to examine energies in
structures. These include color-coded displays written
data and graphs of interaction potentials.
g: geometry examination
d: toggle minimization <-> dynamics
Here, the user can specify whether he wants to do a
energy minimization or a dynamics run. The actual
choice is indicated through the menu title which reads
'mab\q or \qdab\q respectively. Some of the options have
different meaning for the two cases.
l: write protocol item onto file
The current parameters are written as an item onto a
protocol file. They are either written on a new file or
appended on an existing one.
Check H-atom Counts [hyd]
Energy Examination
d: PostScript file
Makes an Encapsulated PostScript file (.eps) of the
current view to be sent to a printer.
b: bonds
Valence bond stretching energies are indicated by the
color of the bonds.
v: valence ang.
Angle bending energies are indicated by colored ring
markers on the atoms.
t: torsion ang.
Dihedral strain energies are indicated by colored
bonds.
p: pyramidalities
*,1,2: all, intra, inter
Non-bonded interaction contributions can be displayed
either within entries only (1), between mutually dis
tinct entries only (2), or both together (*).
r: repulsive v.d.Waals
Between pairs of atoms that experience a positive
v.d.Waals energy a colored dashed line is drawn.
k: attractive v.d.Waals
Between pairs of atoms that experience a negative
v.d.Waals energy a colored dashed line is drawn. This
gives usually a very loaded display
c: repulsive Coulomb
Between pairs of atoms that experience a repulsive Cou
lomb energy a colored dashed line is drawn.
q: attractive Coulomb
Between pairs of atoms that experience a attractive
Coulomb energy a colored dashed line is drawn.
a: atomic charges
If this menu item is chosen, existing charge values for
the atoms are overwritten! The charges are the ones
produced by the setup calculation from which the force
field parameters are derived. Since this calculation
takes into account hybridization dipoles, the resulting
atomic charges tend to be smaller than the ones used in
conventional atomic point charge representations. The
total dipole moment given includes these hybridization
dipoles as well as corrections for the contributions
from the silent hydrogens.
When using the old force field, a electronegativity-
based atomic charge calculation is performed which is a
somewhat modified version of the algorithm proposed by
Gasteiger and Marsili. In this case the dipole moment
is obtained directly from the resulting point charges.
h: H-bonds
Between pairs of atoms that form a hydrogen bond a col
ored dashed line is drawn. The dashes are long at the
donor atom and shorten towards the acceptor.
s: set energy scale
A default energy scale is provided which depends on the
type of interaction examined. The scale and color cod
ing are given in the menu bar. A logarithmic scale
applies such that adjacent colors correspond to a fac
tor of two in energy. If the user redefines the energy
display threshold, this definition only holds for the
next display selection.
e: evaluate entries
For each active entry torsional and 1-4 interactions
are evaluated and printed out. Then, two tables are
generated which sum up van der Waals interaction- and
hydrogen bonding energies respectively. They are
detailed as intra-entry contributions (diagonal ele
ments of the tables) and inter-entry contributions
(off-diagonal). In order not to emphasize short-dis
tance repulsion in the v.d.W terms (which may originate
from insufficient structure precision), all atom pairs
at distances below the v.d.W. minimum contribute an
energy corresponding to the v.d.W. minimum.
w: write data
If precise values of the detailed energy contributions
are needed, this option may be chosen. It gives the var
ious contributions to the energy terms together with
actual and reference values.
g: graphs of the potentials
For a selection of the interaction terms the mathemati
cal form can be obtained as a graphical representation.
l: legend toggle
The energy legend displayed in the lower right hand
corner can be made to disappear.
z: gradient display
The current gradient of the force field can be dis
played in the form of lines extending from each atom.
o: orbitals
By picking any atom which is member of a Pi-system, the
program prints data of the system and a new menu appears
in which the various pi-orbitals can be displayed.
n: normal modes of deformation
The normal modes of deformation are calculated. For
large systems this is a time-consuming calculation! A
spectrum of the modes is produced (units kcal/A**2).
For systems (of more than two atoms) in a local energy
minimum there will be six modes of zero eigenvalue cor
responding to translation and rotation of the system as
a whole. The rest will have positive eigenvalues which
characterize the reluctance of the system to undergo
the corresponding deformation. Large systems show a
quadratic rise of the spectrum, the so-called hydrody
namic regime. If the system is not in a local energy
minimum a few negative eigenvalues usually show up.
Set Constraints [ctr]
s: suspend constraints
This is a possible way to quit this menu. The specified
constraints are kept, but will not be applied in the
energy evaluation. The constraints can be reactivated
by reentering the menu and leaving it with option x.
a: atom positions
For each picked atom a positional constraint is intro
duced with its actual coordinates as the target posi
tion. To induce a positional constraint to a different
position, the user can define a zero-distance con
straint to an atom of a non-active entry.
d: distances
Distance constraints involve two atoms which must be
picked. Then the target distance must be entered. The
default is the sum of the two van der Waals radii. If a
negative value is entered, a docking H-bond is implied.
This type of constraint also enforces the appropriate
directionality of a H-bond.
z: zero-distance (match pairs)
For matching purposes zero-distance constraints are
often needed. This option speeds up setting these, by
not asking for distances.
t: torsions
By picking four consecutive atoms a torsional con
straint is specified.The desired value for the tor
sional angle must be entered together with a quantity,
called 'free\q, that specifies a (two sided) range about
that angle, within which no constraining torque is
applied.
p: pyramidalities
By picking a center and three ligand atoms a pyramidal
constraint is specified. The desired value for the
pyramidality must be entered and a quantity 'free',
that specifies a (two sided) range about that value,
within which no force is applied.
h: homology constraints
Homology constraints are zero-distance constraints
between to polymer entries. The target can be a c-alpha
structure. To define them, a homology file (.alg) is
needed which relates the two corresponding entries. To
apply these constraints click the two entries in the
order in which they appear in the homology file. Then
the program will ask for the name of the homology file.
n: NOE constraints
Read in .upl or .lol files to define upper or lower
bounds. The constraints specification is expected in
the nomenclature of the DIANA program package.
m: modify existing constraints
Previously set constraints can be modified. For each
type of constraint, which is chosen to be modified, a
list of the actual constraints is presented. In this
list the user can choose for each constraint the type of
modification. The list of modification types depends on
the type of the constraint and always includes d for
deletion. The letter v indicates that the numerical
value can be changed. More specific changes include
[l,u,b] for distance constraints (lower, upper, both),
[f] for the free range of torsional and pyramidal con
straints, and [o,n] for alignment constraints (ori
ented, not-oriented).
c: clear constraints
A choice table with the various types of currently
applied constraints is presented. The chosen ones will
be removed.
l: list constraints
A choice table with the various types of currently
applied constraints is presented. For the chosen ones a
detailed list will be printed. A summary is given at the
end.
Running a Protocol and Format of Protocol Files
idn: 0 for minimization, 1 for dynamics.
The optional line with the keyword wgts has the following
form:
In the .mab file a negative value indicates that a pro
tocol is to be executed. The name of the protocol file
is given in fnam.
iter: number of iterations.
For minimizations the output file is overwritten (case
without a protocol) or the structure appended to the
file (if a protocol is running) after each iter itera
tions. By this token the current structure can be exam
ined with the job running (iter = 0 writes only the
final structure).
For dynamics runs new structures are appended to
the result file every 'iter' time steps. This is
repeated 'mrep' times. If mrep = 0 the job keeps append
ing structures indefinitely. For mrep < 0 the job exe
cutes iter time steps but appends no structure to the
file.
mrep: number of repetitions
This parameter is only relevant for dynamics runs (see
under iter, above).
acc: relative accuracy
Determines the level of accuracy at which the minimiza
tion is stopped; only relevant for minimizations.
stp: relative step size
This parameter applies for dynamics only. At room tem
perature a relative step size of one is usually well
working. At more elevated temperatures reduced step
sizes may be necessary for stability reasons.
tmp: temperature parameter (RT in kcal/Mol)
A value of 0.7955 corresponds to 400 K.
masf: mask for fixed atoms
For each atom a mask value is written in the .mab file
just after the coordinates. If this value has a common
bit with the parameter masf, the position of the atom is
held fixed during the force field action.
mask:
This parameter has no effect, and is only added for
analogy to the corresponding protocol for the Calf
force field.
fnam: name of a parameter file
This is only relevant for force field testing, when
parameters should be given alternative values from the
standard ones. In the .mab file this name is taken to be
the protocol file, if the parameter idn is set to a neg
ative value.
MABmask:
As an example the following protocol file leads to a
sequence of three dynamics cycles at 400 K with 1000 time
steps each, which are followed by energy minimizations.
Structures are appended to the result file (.mac) after the
minimization step.
This mask governs several options in the run of the
force field. The value in the examples corresponds to
setting stereochemistry preserving constraints. Values
for the mask are given during interactive setting of
the mask in Moloc.
weights:
The weights are given in logarithmical form, such that a
value of zero will lead to a weight of one. For a value of
less than -99 the weight is set precisely to zero. The values
in the example correspond to standard weights. It is
advisable to generate weight lines in .mab files (partial
job submission, see above).