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 puck1: 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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