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).
Components of this action are:
This input tells plumed to print the puckering phase angle of the second nucleotide of a RNA molecule on file COLVAR.
#SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb MOLINFOPRINT ARG=puck.phs FILE=COLVARSTRUCTURE=rna.pdbcompulsory keyword a file in pdb format containing a reference structure.MOLTYPE=rna puck: PUCKERINGcompulsory keyword ( default=protein ) what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleATOMS=@sugar-2the five or six atoms of the sugar ring in the proper order.
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) |
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 |
NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |