This is part of the colvar module

Calculate sugar pseudorotation coordinates.

This command can be used to calculate ring's pseudorotations in sugars (puckers). It works for both 5-membered and 6-membered rings. Notice that there are two different implementations depending if one passes 5 or 6 atoms in the ATOMS keyword.

For 5-membered rings the implementation is the one discussed in [57] . This implementation is simple and can be used in RNA to distinguish C2'-endo and C3'-endo conformations. Both the polar coordinates (phs and amp) and the Cartesian coordinates (Zx and Zy) are provided. C2'-endo conformations have negative Zx, whereas C3'-endo conformations have positive Zy. Notation is consistent with [57] . The five atoms should be provided as C4',O4',C1',C2',C3'. Notice that this is the same order that can be obtained using the MOLINFO syntax (see example below).

For 6-membered rings the implementation is the general Cremer-Pople one [39] as also discussed in [13] . This implementation provides both a triplet with Cartesian components (qx, qy, and qz) and a triplet of polar components (amplitude, phi, and theta). Applications of this particular implementation are to be published (paper in preparation).

Note: The 6-membered ring implementation distributed with previous versions of PLUMED lead to qx and qy values that had an opposite sign with respect to those originally defined in [39]. The bug is fixed in version 2.5.

Components of this action are:

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
phs	Pseudorotation phase (5 membered rings)
amp	Pseudorotation amplitude (5 membered rings)
Zx	Pseudorotation x Cartesian component (5 membered rings)
Zy	Pseudorotation y Cartesian component (5 membered rings)
phi	Pseudorotation phase (6 membered rings)
theta	Theta angle (6 membered rings)
amplitude	Pseudorotation amplitude (6 membered rings)
qx	Cartesian component x (6 membered rings)
qy	Cartesian component y (6 membered rings)
qz	Cartesian component z (6 membered rings)

The atoms involved can be specified using

ATOMS

the five or six atoms of the sugar ring in the proper order. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

Examples

This input tells plumed to print the puckering phase angle of the 3rd nucleotide of a RNA molecule on file COLVAR.

 #SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb
 MOLINFO STRUCTURE=rna.pdb MOLTYPE=rna
 PUCKERING ATOMS=@sugar-2 LABEL=puck
 PRINT ARG=puck.phs FILE=COLVAR