trajin GAAC3-strip.crd 1 10000 1

center :1-18 mass origin
image origin center familiar
center :1-36 mass origin
image origin center familiar
rms first mass out rms :1-36

prnlev 3

#
#  backbone + sugar
#
donor mask @O1P
donor mask @O2P
donor mask @O3'
donor mask @O5'
donor mask @O4'

acceptor mask :18@O3' :18@H3T
acceptor mask :36@O3' :36@H3T
acceptor mask :1@O5'  :1@H5T
acceptor mask :19@O5' :19@H5T

#
#  minor groove
#
donor DG  N3
donor DG5 N3
donor DG3 N3

donor DA  N3
donor DA5 N3
donor DA3 N3

donor DC  O2
donor DC5 O2
donor DC3 O2

donor DT  O2
donor DT5 O2
donor DT3 O2

acceptor DG  N2 H22
acceptor DG3 N2 H22
acceptor DG5 N2 H22

#
#  base pairing
#
donor DC  N3
donor DC5 N3
donor DC3 N3

donor DA  N1
donor DA5 N1
donor DA3 N1

acceptor DA  N6 H61
acceptor DA3 N6 H61
acceptor DA5 N6 H61

acceptor DC  N4 H41
acceptor DC3 N4 H41
acceptor DC5 N4 H41

acceptor DG  N1 H1
acceptor DG3 N1 H1
acceptor DG5 N1 H1

acceptor DT  N3 H3
acceptor DT3 N3 H3
acceptor DT5 N3 H3

#
#  major groove
#
donor DG  O6
donor DG5 O6
donor DG3 O6

donor DG  N7
donor DG5 N7
donor DG3 N7

donor DA  N7
donor DA5 N7
donor DA3 N7

acceptor DA  N6 H62
acceptor DA3 N6 H62
acceptor DA5 N6 H62

donor DT  O4
donor DT5 O4
donor DT3 O4

acceptor DC  N4 H42
acceptor DC3 N4 H42
acceptor DC5 N4 H42

prnlev 0

hbond series hbond out hbond_k.out \
   solventdonor K+ K+ \
   solventacceptor K+ K+ K+ \
   time 1.0 angle -1.0 distance 3.5

hbond series hbond out hbond_cl.out \
   solventdonor Cl- Cl- \
   solventacceptor Cl- Cl- Cl- \
   time 1.0 angle -1.0 distance 3.5

