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Dihedral Angle Restraints

This section shows how to restrain dihedral angles to particular values. The functional form of the effective energy $E_{CDIH}$ is given by
\begin{displaymath} E_{CDIH}= S \sum C \; {well(modulo_{2\pi}(\phi-{\phi_o}), \Delta\phi)}^{ed} \end{displaymath} (7.3)

where the sum extends over all restrained dihedral angles and the square-well potential $well(a,b)$ is given by
\begin{displaymath} well(a,b) = \left\{ \begin{array}{ll} a-b & \mbox{if $a > b... ...a < b$ } \\ a+b & \mbox{if $a < -b$ } \end{array} \right. \end{displaymath} (7.4)

$S$ is an overall weight factor. The constant $C$, the angle range $\Delta \phi$, the angle centroid $\phi_o$, and the exponent $ed$ are specified in the restraints dihedral statement. The dihedral angle can be defined by a set of four atoms independent of the molecular structure. In particular, the four atoms do not have to be connected to each other. Each atom is selected by a separate selection statement. The dihedral angle involving four atoms i,j,k,l is defined as the angle between two planes, where the first plane is made by atoms i,j,k and the other plane is made by atoms j,k,l.


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Xplor-NIH 2025-03-21