PUCKERING

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 [53] . 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 [53] . 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 [34] as also discussed in [15] . 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 [34]. The bug is fixed in version 2.5.

Components of this action are:

Examples

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

Click on the labels of the actions for more information on what each action computes

#SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb
MOLINFO STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. =rna.pdb MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible =rna The MOLINFO action with label 
puck: PUCKERING ATOMSthe five or six atoms of the sugar ring in the proper order. =@sugar-2 The PUCKERING action with label puck calculates the following quantities:

 Quantity   
 Description  
puck.phs
Pseudorotation phase (5 membered rings)
puck.amp
Pseudorotation amplitude (5 membered rings)
puck.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck.Zy
Pseudorotation y Cartesian component (5 membered rings)


PRINT ARGthe input for this action is the scalar output from one or more other actions. =puck.phs FILEthe name of the file on which to output these quantities =COLVAR The PRINT action with label 

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. 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