MOLINFO STRUCTURE=model.pdb MOLTYPE=rna

t2: TORSION ATOMS=@alpha-2
t3: TORSION ATOMS=@beta-3
t4: TORSION ATOMS=@gamma-4
t5: TORSION ATOMS=@chi-5
t5b: TORSION ATOMS=@chi-6
t5c: TORSION ATOMS=@chi-2
t5d: TORSION ATOMS=@chi-4
t6: TORSION ATOMS=@epsilon-6
t7: TORSION ATOMS=@zeta-7
t8: TORSION ATOMS=@v0-8
t9: TORSION ATOMS=@v1-9
t10: TORSION ATOMS=@v2-10
t11: TORSION ATOMS=@v3-11
t12: TORSION ATOMS=@v4-12

c1: CENTER ATOMS=@base-4
c2: CENTER ATOMS=@base-5
d1: DISTANCE ATOMS=c1,c2
c3: CENTER ATOMS=@base-2
c4: CENTER ATOMS=@base-6
d2: DISTANCE ATOMS=c3,c4

puck1: PUCKERING ATOMS=@sugar-1
puck2: PUCKERING ATOMS=@sugar-2
puck3: PUCKERING ATOMS=@sugar-3
puck4: PUCKERING ATOMS=@sugar-4
puck5: PUCKERING ATOMS=@sugar-5
puck6: PUCKERING ATOMS=@sugar-6
puck7: PUCKERING ATOMS=@sugar-7
puck8: PUCKERING ATOMS=@sugar-8
puck9: PUCKERING ATOMS=@sugar-9
puck10: PUCKERING ATOMS=@sugar-10
puck11: PUCKERING ATOMS=@sugar-11
puck12: PUCKERING ATOMS=@sugar-12
puck13: PUCKERING ATOMS=@sugar-13
puck14: PUCKERING ATOMS=@sugar-14

hb1: DISTANCE ATOMS=@N2-1,@O2-14
hb2: DISTANCE ATOMS=@N1-1,@N3-14
hb3: DISTANCE ATOMS=@O6-1,@N4-14


PRINT ARG=t2,t3,t4,t5,t5b,t5c,t5d,t6,t7,t8,t9,t10,t12,d1,d2,hb1,hb2,hb3 FILE=COLVAR FMT=%6.3f

DUMPDERIVATIVES ...
  ARG=puck1.amp,puck1.phs,puck1.Zx,puck1.Zy,puck2.Zx,puck2.Zy,puck3.Zx,puck3.Zy,puck4.Zx,puck4.Zy,puck5.Zx,puck5.Zy,puck6.Zx,puck6.Zy,puck7.Zx,puck7.Zy,puck8.Zx,puck8.Zy,puck9.Zx,puck9.Zy,puck10.Zx,puck10.Zy,puck11.Zx,puck11.Zy,puck12.Zx,puck12.Zy,puck13.Zx,puck13.Zy,puck14.Zx,puck14.Zy
  FILE=DERIVATIVES 
  FMT=%8.4f
... DUMPDERIVATIVES 

ENDPLUMED
