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
Click on the labels of the actions for more information on what each action computes
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 somethingpuck1The PUCKERING action with label puck1 calculates the following quantities:| Quantity | Type | Description |
| puck1.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck1.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck1.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck1.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-1the heavy atoms of the sugar in residue 1. Click here for more information.
puck2The PUCKERING action with label puck2 calculates the following quantities:| Quantity | Type | Description |
| puck2.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck2.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck2.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck2.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.
puck3The PUCKERING action with label puck3 calculates the following quantities:| Quantity | Type | Description |
| puck3.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck3.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck3.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck3.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-3the heavy atoms of the sugar in residue 3. Click here for more information.
puck4The PUCKERING action with label puck4 calculates the following quantities:| Quantity | Type | Description |
| puck4.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck4.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck4.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck4.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-4the heavy atoms of the sugar in residue 4. Click here for more information.
puck5The PUCKERING action with label puck5 calculates the following quantities:| Quantity | Type | Description |
| puck5.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck5.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck5.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck5.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-5the heavy atoms of the sugar in residue 5. Click here for more information.
puck6The PUCKERING action with label puck6 calculates the following quantities:| Quantity | Type | Description |
| puck6.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck6.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck6.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck6.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-6the heavy atoms of the sugar in residue 6. Click here for more information.
puck7The PUCKERING action with label puck7 calculates the following quantities:| Quantity | Type | Description |
| puck7.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck7.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck7.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck7.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-7the heavy atoms of the sugar in residue 7. Click here for more information.
puck8The PUCKERING action with label puck8 calculates the following quantities:| Quantity | Type | Description |
| puck8.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck8.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck8.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck8.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-8the heavy atoms of the sugar in residue 8. Click here for more information.
puck9The PUCKERING action with label puck9 calculates the following quantities:| Quantity | Type | Description |
| puck9.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck9.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck9.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck9.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-9the heavy atoms of the sugar in residue 9. Click here for more information.
puck10The PUCKERING action with label puck10 calculates the following quantities:| Quantity | Type | Description |
| puck10.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck10.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck10.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck10.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-10the heavy atoms of the sugar in residue 10. Click here for more information.
puck11The PUCKERING action with label puck11 calculates the following quantities:| Quantity | Type | Description |
| puck11.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck11.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck11.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck11.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-11the heavy atoms of the sugar in residue 11. Click here for more information.
puck12The PUCKERING action with label puck12 calculates the following quantities:| Quantity | Type | Description |
| puck12.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck12.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck12.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck12.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-12the heavy atoms of the sugar in residue 12. Click here for more information.
puck13The PUCKERING action with label puck13 calculates the following quantities:| Quantity | Type | Description |
| puck13.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck13.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck13.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck13.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-13the heavy atoms of the sugar in residue 13. Click here for more information.
puck14The PUCKERING action with label puck14 calculates the following quantities:| Quantity | Type | Description |
| puck14.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck14.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck14.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck14.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-14the heavy atoms of the sugar in residue 14. Click here for more information.
puck15The PUCKERING action with label puck15 calculates the following quantities:| Quantity | Type | Description |
| puck15.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck15.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck15.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck15.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-15the heavy atoms of the sugar in residue 15. Click here for more information.
puck16The PUCKERING action with label puck16 calculates the following quantities:| Quantity | Type | Description |
| puck16.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck16.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck16.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck16.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-16the heavy atoms of the sugar in residue 16. Click here for more information.
puck17The PUCKERING action with label puck17 calculates the following quantities:| Quantity | Type | Description |
| puck17.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck17.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck17.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck17.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-17the heavy atoms of the sugar in residue 17. Click here for more information.
puck18The PUCKERING action with label puck18 calculates the following quantities:| Quantity | Type | Description |
| puck18.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck18.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck18.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck18.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-18the heavy atoms of the sugar in residue 18. Click here for more information.
puck19The PUCKERING action with label puck19 calculates the following quantities:| Quantity | Type | Description |
| puck19.phs | scalar | Pseudorotation phase (5 membered rings) |
| puck19.amp | scalar | Pseudorotation amplitude (5 membered rings) |
| puck19.Zx | scalar | Pseudorotation x Cartesian component (5 membered rings) |
| puck19.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-19the heavy atoms of the sugar in residue 19. 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=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
