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.
| Name | Type | Description |
|---|---|---|
| phs | scalar | Pseudorotation phase (5 membered rings) |
| amp | scalar | Pseudorotation amplitude (5 membered rings) |
| Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| Zy | scalar | Pseudorotation y Cartesian component (5 membered rings) |
| phi | scalar | Pseudorotation phase (6 membered rings) |
| theta | scalar | Theta angle (6 membered rings) |
| amplitude | scalar | Pseudorotation amplitude (6 membered rings) |
| qx | scalar | Cartesian component x (6 membered rings) |
| qy | scalar | Cartesian component y (6 membered rings) |
| qz | scalar | Cartesian component z (6 membered rings) |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ATOMS | atoms | the five or six atoms of the sugar ring in the proper order |
Further details and examples
Text from manual goes here
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
| Keyword | Type | Default | Description |
|---|---|---|---|
| ATOMS | input | none | the five or six atoms of the sugar ring in the proper order |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |