Action: PUCKERING

Module	colvar
Description	Usage
Calculate sugar pseudorotation coordinates.

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

Calculate sugar pseudorotation coordinates.

This command can be used to calculate pseudorotations for the rings 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. 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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=
regtest/basic/rt65/AA.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt65/AA.pdb
    
TITLE     Great Red Owns Many ACres of Sand 
REMARK    THIS IS A SIMULATION BOX
CRYST1    6.958   11.030   10.714  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM     1   H5T   A     1      14.820  -3.670   5.260  1.00  0.00            
...
ATOM     63 2HO'   A     2      13.980   7.360   7.150  1.00  0.00            
ATOM     64  O3'   A     2      13.300   5.500   8.180  1.00  0.00            
ATOM     65  H3T   A     2      12.360   5.840   8.100  1.00  0.00            
TER
ENDMDL
  
 MOLTYPE 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  calculates somethingpuckThe PUCKERING action with label puck calculates the following quantities:
 Quantity   
 Type   
 Description  
puck.phs
scalar
Pseudorotation phase (5 membered rings)
puck.amp
scalar
Pseudorotation amplitude (5 membered rings)
puck.Zx
scalar
Pseudorotation x Cartesian component (5 membered rings)
puck.Zy
scalar
Pseudorotation y Cartesian component (5 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-2the heavy atoms of the sugar in residue 2. Click here for more information. 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=puck.phs FILEthe name of the file on which to output these quantities=COLVAR

For 5-membered rings the implementation is the one discussed in the first of the papers in the bibliography below. 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. The notation is consistent with the notation in that first paper. 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 that is discussed in the second and third papers in the bibliography. 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 yet 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 the thid reference in the bibliograph below. The bug was fixed in version 2.5.

References

More information about how this action can be used is available in the following articles: - M. Huang, T. J. Giese, T.-S. Lee, D. M. York, Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods. Journal of Chemical Theory and Computation. 10, 1538–1545 (2014) - D. Cremer, J. A. Pople, General definition of ring puckering coordinates. Journal of the American Chemical Society. 97, 1354–1358 (1975) - X. Biarnés, A. Ardèvol, A. Planas, C. Rovira, A. Laio, M. Parrinello, The Conformational Free Energy Landscape of β-d-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases. Journal of the American Chemical Society. 129, 10686–10693 (2007)

Syntax

The following table describes the keywords and options that can be used with this action