Grid correlate

grid correlate

Parameters

function=string (required)

selection=string

(default: none)

Description

This command defines relationships between dihedral angles in a grid search. For instance, the dihedral angles of a sugar ring can be represented by a single degree of freedom, the pseudorotation angle.

To represent a group of dihedral angles as a single degree of freedom in a grid search, this command has to be called once for each correlated dihedral angle. If exactly one angle within the fragment is matched by the selection parameter, then this dihedral angle will be related by the given function, a Fortran expression of type real, to a variable, p. The variable p will be the single degree of freedom during the grid search during which it will vary from 0 to 2*pi. If exactly two angles within the fragment are selected, one of which has occurred in a previous angle correlate command, then the "new" angle will be correlated by the given function to the same parameter p as the "old" angle.

For example, a molecular fragment consisting of the sugar ring of nucleotide residue 4 in a DNA or RNA molecule can be defined, and the dihedral angles of the sugar ring, DELTA, NU1, and NU2 be correlated to the pseudorotation angle, as follows:

 grid fragment "DELTA NU1 NU2 4"
 numax=40.0*pi/180.0
 grid correlate numax*cos(p+4*pi/5)+2*pi/3 "DELTA 4"
 grid correlate numax*cos(p-4*pi/5) "DELTA NU1 4"
 grid correlate numax*cos(p) "DELTA NU2 4"

See also

• sugarring