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

#G1U37 distances: Hbonds that should be there
distance dist1 :2@N1 :37@O2 A.out time 1.0 
distance dist2 :2@O6 :37@N3 B.out time 1.0 

#G25U20 distances
distance dist3 :21@N3 :26@O6 out E.out time 1.0 
distance dist4 :21@O4 :26@N1 out D.out time 1.0 

#C41quad distances
distance dist5 :41@N4 :60@N7 out F.out time 1.0 
distance dist6 :41@N3 :60@O6 out G.out time 1.0 
distance dist7 :41@O2 :43@N6 out H.out time 1.0 
distance dist8 :41@O2 :44@N4 out I.out time 1.0 

#Active Site distances
#C75(N3)-A1+(O5')
distance dist9 :2@O5' :62@N3 out C.out time 1.0 
#U-1(2O')-A1+phosphate
distance dist10 :1@O2' :2@P out J.out time 1.0