parm ../IIL-amber.pdb
trajin ../IIL-amber.pdb

check @N1,N2,P,OP1,OP2,C1',C2',C3',C4',O3',O4' skipbadframes silent

pwd
pwd

rms fit :1-24

multidihedral dih alpha beta gamma delta epsilon zeta chin resrange 1-24
multidihedral dih360 alpha beta gamma delta epsilon zeta chin resrange 1-24 range360

nastruct NA1 resrange 1-24 groovecalc 3dna

run

#base pair parameters
writedata shear.dat NA1[shear]
writedata stretch.dat NA1[stretch]
writedata stagger.dat NA1[stagger]
writedata buckle.dat NA1[buckle]
writedata prop.dat NA1[prop]
writedata opening.dat NA1[open]

#base step parameters
writedata shift.dat NA1[shift]
writedata tilt.dat NA1[tilt]
writedata slide.dat NA1[slide]
writedata rise.dat NA1[rise]
writedata roll.dat NA1[roll]
writedata twist.dat NA1[twist]

#helical parameters
writedata xdisp.dat NA1[xdisp]
writedata ydisp.dat NA1[ydisp]
writedata helical-rise.dat NA1[hrise]
writedata helical-inclination.dat NA1[incl]
writedata tip.dat NA1[tip]
writedata helical-twist.dat NA1[htwist]

#groove widths
writedata major.dat NA1[major]
writedata minor.dat NA1[minor]

#pucker
writedata pucker.dat NA1[pucker]

#hydrogen bonds between bases
writedata hb.dat NA1[hb]

# Backbone dihedrals
writedata alpha.dat dih[alpha]
writedata beta.dat dih[beta]
writedata gamma.dat dih[gamma]
writedata delta.dat dih[delta]
writedata epsilon.dat dih[epsilon]
writedata zeta.dat dih[zeta]
writedata chi.dat dih[chin]

writedata alpha.360.dat dih360[alpha]
writedata beta.360.dat dih360[beta]
writedata gamma.360.dat dih360[gamma]
writedata delta.360.dat dih360[delta]
writedata epsilon.360.dat dih360[epsilon]
writedata zeta.360.dat dih360[zeta]
writedata chi.360.dat dih360[chin]