Project ID: plumID:24.028
Source: inputs/tip3p/quadruplex/metadyn/plumed_pucker.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
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=../conf.pdb 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 somethingpuck1: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-1the heavy atoms of the sugar in residue 1. Click here for more information.
The PUCKERING action with label puck1 calculates the following quantities:| Quantity | Description |
| puck1.phs | Pseudorotation phase (5 membered rings) |
| puck1.amp | Pseudorotation amplitude (5 membered rings) |
| puck1.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck1.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck1.phi | Pseudorotation phase (6 membered rings) |
| puck1.theta | Theta angle (6 membered rings) |
| puck1.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck1.qx | Cartesian component x (6 membered rings) |
| puck1.qy | Cartesian component y (6 membered rings) |
| puck1.qz | Cartesian component z (6 membered rings) |
puck2: 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.
The PUCKERING action with label puck2 calculates the following quantities:| Quantity | Description |
| puck2.phs | Pseudorotation phase (5 membered rings) |
| puck2.amp | Pseudorotation amplitude (5 membered rings) |
| puck2.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck2.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck2.phi | Pseudorotation phase (6 membered rings) |
| puck2.theta | Theta angle (6 membered rings) |
| puck2.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck2.qx | Cartesian component x (6 membered rings) |
| puck2.qy | Cartesian component y (6 membered rings) |
| puck2.qz | Cartesian component z (6 membered rings) |
puck3: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-3the heavy atoms of the sugar in residue 3. Click here for more information.
The PUCKERING action with label puck3 calculates the following quantities:| Quantity | Description |
| puck3.phs | Pseudorotation phase (5 membered rings) |
| puck3.amp | Pseudorotation amplitude (5 membered rings) |
| puck3.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck3.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck3.phi | Pseudorotation phase (6 membered rings) |
| puck3.theta | Theta angle (6 membered rings) |
| puck3.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck3.qx | Cartesian component x (6 membered rings) |
| puck3.qy | Cartesian component y (6 membered rings) |
| puck3.qz | Cartesian component z (6 membered rings) |
puck4: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-4the heavy atoms of the sugar in residue 4. Click here for more information.
The PUCKERING action with label puck4 calculates the following quantities:| Quantity | Description |
| puck4.phs | Pseudorotation phase (5 membered rings) |
| puck4.amp | Pseudorotation amplitude (5 membered rings) |
| puck4.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck4.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck4.phi | Pseudorotation phase (6 membered rings) |
| puck4.theta | Theta angle (6 membered rings) |
| puck4.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck4.qx | Cartesian component x (6 membered rings) |
| puck4.qy | Cartesian component y (6 membered rings) |
| puck4.qz | Cartesian component z (6 membered rings) |
puck5: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-5the heavy atoms of the sugar in residue 5. Click here for more information.
The PUCKERING action with label puck5 calculates the following quantities:| Quantity | Description |
| puck5.phs | Pseudorotation phase (5 membered rings) |
| puck5.amp | Pseudorotation amplitude (5 membered rings) |
| puck5.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck5.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck5.phi | Pseudorotation phase (6 membered rings) |
| puck5.theta | Theta angle (6 membered rings) |
| puck5.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck5.qx | Cartesian component x (6 membered rings) |
| puck5.qy | Cartesian component y (6 membered rings) |
| puck5.qz | Cartesian component z (6 membered rings) |
puck6: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-6the heavy atoms of the sugar in residue 6. Click here for more information.
The PUCKERING action with label puck6 calculates the following quantities:| Quantity | Description |
| puck6.phs | Pseudorotation phase (5 membered rings) |
| puck6.amp | Pseudorotation amplitude (5 membered rings) |
| puck6.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck6.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck6.phi | Pseudorotation phase (6 membered rings) |
| puck6.theta | Theta angle (6 membered rings) |
| puck6.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck6.qx | Cartesian component x (6 membered rings) |
| puck6.qy | Cartesian component y (6 membered rings) |
| puck6.qz | Cartesian component z (6 membered rings) |
puck7: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-7the heavy atoms of the sugar in residue 7. Click here for more information.
The PUCKERING action with label puck7 calculates the following quantities:| Quantity | Description |
| puck7.phs | Pseudorotation phase (5 membered rings) |
| puck7.amp | Pseudorotation amplitude (5 membered rings) |
| puck7.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck7.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck7.phi | Pseudorotation phase (6 membered rings) |
| puck7.theta | Theta angle (6 membered rings) |
| puck7.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck7.qx | Cartesian component x (6 membered rings) |
| puck7.qy | Cartesian component y (6 membered rings) |
| puck7.qz | Cartesian component z (6 membered rings) |
puck8: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-8the heavy atoms of the sugar in residue 8. Click here for more information.
The PUCKERING action with label puck8 calculates the following quantities:| Quantity | Description |
| puck8.phs | Pseudorotation phase (5 membered rings) |
| puck8.amp | Pseudorotation amplitude (5 membered rings) |
| puck8.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck8.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck8.phi | Pseudorotation phase (6 membered rings) |
| puck8.theta | Theta angle (6 membered rings) |
| puck8.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck8.qx | Cartesian component x (6 membered rings) |
| puck8.qy | Cartesian component y (6 membered rings) |
| puck8.qz | Cartesian component z (6 membered rings) |
puck9: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-9the heavy atoms of the sugar in residue 9. Click here for more information.
The PUCKERING action with label puck9 calculates the following quantities:| Quantity | Description |
| puck9.phs | Pseudorotation phase (5 membered rings) |
| puck9.amp | Pseudorotation amplitude (5 membered rings) |
| puck9.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck9.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck9.phi | Pseudorotation phase (6 membered rings) |
| puck9.theta | Theta angle (6 membered rings) |
| puck9.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck9.qx | Cartesian component x (6 membered rings) |
| puck9.qy | Cartesian component y (6 membered rings) |
| puck9.qz | Cartesian component z (6 membered rings) |
puck10: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-10the heavy atoms of the sugar in residue 10. Click here for more information.
The PUCKERING action with label puck10 calculates the following quantities:| Quantity | Description |
| puck10.phs | Pseudorotation phase (5 membered rings) |
| puck10.amp | Pseudorotation amplitude (5 membered rings) |
| puck10.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck10.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck10.phi | Pseudorotation phase (6 membered rings) |
| puck10.theta | Theta angle (6 membered rings) |
| puck10.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck10.qx | Cartesian component x (6 membered rings) |
| puck10.qy | Cartesian component y (6 membered rings) |
| puck10.qz | Cartesian component z (6 membered rings) |
puck11: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-11the heavy atoms of the sugar in residue 11. Click here for more information.
The PUCKERING action with label puck11 calculates the following quantities:| Quantity | Description |
| puck11.phs | Pseudorotation phase (5 membered rings) |
| puck11.amp | Pseudorotation amplitude (5 membered rings) |
| puck11.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck11.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck11.phi | Pseudorotation phase (6 membered rings) |
| puck11.theta | Theta angle (6 membered rings) |
| puck11.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck11.qx | Cartesian component x (6 membered rings) |
| puck11.qy | Cartesian component y (6 membered rings) |
| puck11.qz | Cartesian component z (6 membered rings) |
puck12: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-12the heavy atoms of the sugar in residue 12. Click here for more information.
The PUCKERING action with label puck12 calculates the following quantities:| Quantity | Description |
| puck12.phs | Pseudorotation phase (5 membered rings) |
| puck12.amp | Pseudorotation amplitude (5 membered rings) |
| puck12.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck12.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck12.phi | Pseudorotation phase (6 membered rings) |
| puck12.theta | Theta angle (6 membered rings) |
| puck12.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck12.qx | Cartesian component x (6 membered rings) |
| puck12.qy | Cartesian component y (6 membered rings) |
| puck12.qz | Cartesian component z (6 membered rings) |
puck13: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-13the heavy atoms of the sugar in residue 13. Click here for more information.
The PUCKERING action with label puck13 calculates the following quantities:| Quantity | Description |
| puck13.phs | Pseudorotation phase (5 membered rings) |
| puck13.amp | Pseudorotation amplitude (5 membered rings) |
| puck13.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck13.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck13.phi | Pseudorotation phase (6 membered rings) |
| puck13.theta | Theta angle (6 membered rings) |
| puck13.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck13.qx | Cartesian component x (6 membered rings) |
| puck13.qy | Cartesian component y (6 membered rings) |
| puck13.qz | Cartesian component z (6 membered rings) |
puck14: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-14the heavy atoms of the sugar in residue 14. Click here for more information.
The PUCKERING action with label puck14 calculates the following quantities:| Quantity | Description |
| puck14.phs | Pseudorotation phase (5 membered rings) |
| puck14.amp | Pseudorotation amplitude (5 membered rings) |
| puck14.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck14.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck14.phi | Pseudorotation phase (6 membered rings) |
| puck14.theta | Theta angle (6 membered rings) |
| puck14.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck14.qx | Cartesian component x (6 membered rings) |
| puck14.qy | Cartesian component y (6 membered rings) |
| puck14.qz | Cartesian component z (6 membered rings) |
puck15: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-15the heavy atoms of the sugar in residue 15. Click here for more information.
The PUCKERING action with label puck15 calculates the following quantities:| Quantity | Description |
| puck15.phs | Pseudorotation phase (5 membered rings) |
| puck15.amp | Pseudorotation amplitude (5 membered rings) |
| puck15.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck15.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck15.phi | Pseudorotation phase (6 membered rings) |
| puck15.theta | Theta angle (6 membered rings) |
| puck15.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck15.qx | Cartesian component x (6 membered rings) |
| puck15.qy | Cartesian component y (6 membered rings) |
| puck15.qz | Cartesian component z (6 membered rings) |
puck16: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-16the heavy atoms of the sugar in residue 16. Click here for more information.
The PUCKERING action with label puck16 calculates the following quantities:| Quantity | Description |
| puck16.phs | Pseudorotation phase (5 membered rings) |
| puck16.amp | Pseudorotation amplitude (5 membered rings) |
| puck16.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck16.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck16.phi | Pseudorotation phase (6 membered rings) |
| puck16.theta | Theta angle (6 membered rings) |
| puck16.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck16.qx | Cartesian component x (6 membered rings) |
| puck16.qy | Cartesian component y (6 membered rings) |
| puck16.qz | Cartesian component z (6 membered rings) |
puck17: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-17the heavy atoms of the sugar in residue 17. Click here for more information.
The PUCKERING action with label puck17 calculates the following quantities:| Quantity | Description |
| puck17.phs | Pseudorotation phase (5 membered rings) |
| puck17.amp | Pseudorotation amplitude (5 membered rings) |
| puck17.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck17.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck17.phi | Pseudorotation phase (6 membered rings) |
| puck17.theta | Theta angle (6 membered rings) |
| puck17.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck17.qx | Cartesian component x (6 membered rings) |
| puck17.qy | Cartesian component y (6 membered rings) |
| puck17.qz | Cartesian component z (6 membered rings) |
puck18: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-18the heavy atoms of the sugar in residue 18. Click here for more information.
The PUCKERING action with label puck18 calculates the following quantities:| Quantity | Description |
| puck18.phs | Pseudorotation phase (5 membered rings) |
| puck18.amp | Pseudorotation amplitude (5 membered rings) |
| puck18.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck18.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck18.phi | Pseudorotation phase (6 membered rings) |
| puck18.theta | Theta angle (6 membered rings) |
| puck18.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck18.qx | Cartesian component x (6 membered rings) |
| puck18.qy | Cartesian component y (6 membered rings) |
| puck18.qz | Cartesian component z (6 membered rings) |
puck19: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-19the heavy atoms of the sugar in residue 19. Click here for more information.
The PUCKERING action with label puck19 calculates the following quantities:| Quantity | Description |
| puck19.phs | Pseudorotation phase (5 membered rings) |
| puck19.amp | Pseudorotation amplitude (5 membered rings) |
| puck19.Zx | Pseudorotation x Cartesian component (5 membered rings) |
| puck19.Zy | Pseudorotation y Cartesian component (5 membered rings) |
| puck19.phi | Pseudorotation phase (6 membered rings) |
| puck19.theta | Theta angle (6 membered rings) |
| puck19.amplitude | Pseudorotation amplitude (6 membered rings) |
| puck19.qx | Cartesian component x (6 membered rings) |
| puck19.qy | Cartesian component y (6 membered rings) |
| puck19.qz | Cartesian component z (6 membered rings) |
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=puck1.Zx,puck2.Zx,puck3.Zx,puck4.Zx,puck5.Zx,puck6.Zx,puck7.Zx,puck8.Zx,puck9.Zx,puck10.Zx,puck11.Zx,puck12.Zx,puck13.Zx,puck14.Zx,puck15.Zx,puck16.Zx,puck17.Zx,puck18.Zx,puck19.Zx FILEthe name of the file on which to output these quantities=ANALYSIS_PUCKERING
