trajin x.crd trajin ../production1.traj.gz trajin ../production2.traj.gz # To center and image the molecule center :1-73 mass origin image origin center #In-line attack angle: U-1(2O'), N1(P), N1(O5') angle dist11 :1@O2' :2@P :2@O5' out IAA.out time 1.0 #Extra Hbonds distance dist12 :2@2O' :37@N2 out x.out time 1.0 #Dihedrals: delta epsilon zeta (not done in ion_density script) #Delta: U-1(C5', C4', C3', O3') dihedral dist13 :1@C5' :1@C4' :1@C3' :1@O3' out delta_U-1 #Epsilon: U-1(C4', C3', O3'), N1(P) dihedral dist14 :1@C4' :1@C3' :1@O3' :2@P out epsilon_U-1 #Zeta: U-1(C3', O3'), N1(P, O5') dihedral dist15 :1@C3' :1@O3' :2@P :2@O5' out zeta_U-1