# rms analysis omitting terminal 2 base pairs
# reference = respective pdb structure (start.pdb)

parm nowater.topo
trajin aggregate.nc 1 last 10
check @N1,N2,P,OP1,OP2,C1',C2',C3',C4',O3',O4' skipbadframes silent

reference start.pdb

rms reference :1-24&!@H= out data/rms_ref.dat time 200
rms reference :3-10,15-22&!@H= out data/rms_ref-internal.dat time 20

atomicfluct out data/fluct_byatom_bfactor.dat :1-24 bfactor
atomicfluct out data/fluct_byres_bfactor.dat :1-24 byres bfactor
atomicfluct out data/fluct_byatom.dat :1-24
atomicfluct out data/fluct_byres.dat :1-24 byres

go
clear all

# nastruct analysis omitting terminal 2 base pairs
# reference = respective pdb structure (start.pdb)

parm nowater.topo
trajin aggregate.nc 1 last 10
check @N1,N2,P,OP1,OP2,C1',C2',C3',C4',O3',O4' skipbadframes silent

reference start.pdb

nastruct NA1 reference resrange 3-10,15-22
run

writedata data/major.dat NA1[major]
writedata data/minor.dat NA1[minor]
writedata data/helical-twist.dat NA1[htwist]
writedata data/helical-inclination.dat NA1[incl]
writedata data/hb.dat NA1[hb]
writedata data/shear.dat NA1[shear]
writedata data/buckle.dat NA1[buckle]
writedata data/stretch.dat NA1[stretch]
writedata data/stagger.dat NA1[stagger]
writedata data/prop.dat NA1[prop]
writedata data/opening.dat NA1[open]
writedata data/shift.dat NA1[shift]
writedata data/tilt.dat NA1[tilt]
writedata data/slide.dat NA1[slide]
writedata data/rise.dat NA1[rise]
writedata data/roll.dat NA1[roll]
writedata data/twist.dat NA1[twist]