Minimax provides six types of constraints: distance, angle, projections,
volume, torsion and fixed atom constraint. The definitions of the constraints
are read in from file molecule.con (-C option) or the file
named by the -Cf option. The constraints file is free format. The
first character of each line of the file determines the type of constraint
(D:distance, A:angle, P:projection, T:torsion,
F:fixed
atom, V:volume). Blank lines are ignored, lines with a C
in column 1 are treated as comment, and an E in column 1 is accepted
as end-of-file (optional).
Distance constraints:
dmin < d i,j < dmax , where d i,j is the distance (Å) between atoms i and j.Implemented by adding a harmonic penalty function to the total energy:
E penalty = 0.5 * k i,j * (max{0,dmin - d i,j} + max{0,d i,j - dmax}) 2
Definition in constraints file: (i and j are atom sequence numbers)Angle constraints:D i j dmin dmax ki,j
amin < a i,j,k < amax , where a i,j,k is the angle (deg.) between atoms i,j,kImplemented by adding a harmonic penalty function to the total energy:
E penalty = 0.5 * k i,j,k * (max{0,amin - a i,j,k} + max{0,a i,j,k - amax}) 2
Definition in constraints file: (i, i, k are atom sequence numbers)Torsion constraints:A i j k amin amax ki,j,k,l
tmin < t i,j,k,l < tmax , where t i,j,k,l is the dihedral angle (deg.) between atoms i,j,k,lImplemented by adding a harmonic penalty function to the total energy:
E penalty = 0.5 * k i,j,k,l * (max{0,tmin - t i,j,k,l} + max{0,t i,j,k,l - tmax}) 2
Definition in constraints file: (i, j, k, l are atom sequence numbers)T i j k l tmin tmax ki,j,k,l
Note: tmin must not exceed tmax, and tmin must lie in the interval [-180,+180].
Volume constraints:
V i,j,k,l > Vmin , where V i,k,k,l is the (signed) parallelepipedial product <(xj-xi)*(xk-xi),xl-xi> , and xi, xi, xk, xl are the coordinate vectors of atoms i,k,k and l.Fixed atom constraints:Implemented by adding a harmonic penalty function to the total energy:
E penalty = k i,j,k,l * max{0,Vmin - V i,j,k,l}2
Definition in constraints file: (i, j, k ,l are atom sequence numbers)
V i j k l Vmin ki,j,k,l
Note: used judiciously, this may be used as a chirality constraint. Indeed, this type of constraint is used by the -Cs option ("preserver chirality").
Atoms listed in fixed atom constraints will be kept fixed during energy minimization. Only energy terms involving at least one variable (non-fixed) atom will be computed.Projection constraints:Definition in constraints file: (i, j, k, l, m ... are atom sequence numbers)
F i j k l m n ....
Where i,j,k,l,m,n,... are the sequence numbers of the atoms to be fixed (up to 256 numbers per line).
dx,yi,j = c*p i,j , where dx,yi,j is the distance between atoms i and j in the orthogonal projection onto the (x,y) plane.Implemented by adding a harmonic penalty function to the total energy:
E penalty = 0.5*k i,j* (dx,yi,j - c*p i,j )2
Definition in constraints file: (i and j are atom sequence numbers)
P i j pi,j ki,j
Note: The parameter c is a 'scale' which will be adjusted by the program to minimize the constraint violations. Projection constraints can be used to build 3D models that fulfill 2D constraints, e.g. projected distances measured in figures from publications.
Positional constraints:
A soft sqare-well penalty function may be used to constrain atomic positions to reference positions.Epenalty = 0.5 * ki * DH2 + ki * DH * DL , where
DH = max { min { di - T , L } , 0 } , and DL = max { di - DH - T , 0 } ,
and di is the distance from the reference point (xr , yr , zr ).
Definition in constraints file: ( i is the sequence number of the atom that is constrained):
X i [ xr yr zr ] ki [ T [ L ] ]
If no reference point is specified, the atom will be constrained to the initial position. The tolerance T defaults to 0, the default for L (switch-over to linear) is at infinity.