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#trajin traj.1
#trajin traj.2
#trajin traj.3
#trajin traj.4
trajin traj.5 28 99999 1
trajin traj.6
trajin traj.7 1 28 1
#trajin traj.8
#trajin traj.9
#trajin traj.10
center :1-17 mass origin
image origin center
rms first mass :1-17

prnlev 2

donor RU  O2
donor RU5 O2
donor RU3 O2

donor RU  O4
donor RU5 O4
donor RU3 O4

donor RA  N1
donor RA5 N1
donor RA3 N1

donor RA  N3
donor RA5 N3
donor RA3 N3

donor RA  N7
donor RA5 N7
donor RA3 N7

donor RC  N3
donor RC5 N3
donor RC3 N3

donor RC  O2
donor RC5 O2
donor RC3 O2

donor RG  O6
donor RG5 O6
donor RG3 O6

donor RG  N3
donor RG5 N3
donor RG3 N3

donor RG  N7
donor RG5 N7
donor RG3 N7

donor U8U O4
donor U8U S2

acceptor U8U N3 H3
acceptor U8U N  HN
acceptor U8U N  HN2

donor T6A N3
donor T6A N7
donor T6A O14
donor T6A O13A
donor T6A O13B
donor T6A O10

acceptor T6A N6 H6
acceptor T6A O14 HO4

donor PSU O2
donor PSU O4

acceptor PSU N3 H3
acceptor PSU N1 H1

acceptor RU  N6 H61
acceptor RU5 N6 H61
acceptor RU3 N6 H61

acceptor RU  N6 H62
acceptor RU5 N6 H62
acceptor RU3 N6 H62

acceptor RU  N3 H3
acceptor RU5 N3 H3
acceptor RU3 N3 H3

acceptor RC  N4 H41
acceptor RC5 N4 H41
acceptor RC3 N4 H41

acceptor RC  N4 H42
acceptor RC5 N4 H42
acceptor RC3 N4 H42

acceptor RA  C2 H2
acceptor RA5 C2 H2
acceptor RA3 C2 H2

acceptor RA  N6 H61
acceptor RA5 N6 H61
acceptor RA3 N6 H61

acceptor RA  N6 H62
acceptor RA5 N6 H62
acceptor RA3 N6 H62

acceptor RG  N1 H1
acceptor RG5 N1 H1
acceptor RG3 N1 H1

acceptor RG  N2 H21
acceptor RG5 N2 H21
acceptor RG3 N2 H21

acceptor RG  N2 H22
acceptor RG5 N2 H22
acceptor RG3 N2 H22

donor mask @O2'
donor mask @O3'
donor mask @O4'
donor mask @O5'
donor mask @O1P
donor mask @O2P
acceptor mask @O2' @HO'2

prnlev 0

hbond series hbond out hbond.out time 1.0 distance 3.5 angle 120.0

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