#!/bin/tcsh
# This is an example which calculates the Jcoupling for chi dihedrals in a dinucleotide
cat << EOF > pt-jcoupling.in
parm ../../build/full.topo.hmr [traj]

autoimage origin

trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18  

dihedral chi1_c4 :1@H1' :1@C1' :1@N9 :1@C4 out diheds.dat 
dihedral chi1_c8 :1@H1' :1@C1' :1@N9 :1@C8 out diheds.dat
dihedral chi2_c4 :2@H1' :2@C1' :2@N9 :2@C4 out diheds.dat
dihedral chi2_c8 :2@H1' :2@C1' :2@N9 :2@C8 out diheds.dat
dihedral ep1_c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat
dihedral ep1_c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat
dihedral ep1_h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat
dihedral beta2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat
dihedral gamma1 :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat
dihedral delta1 :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat
dihedral delta2 :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat

jcoupling name jcoup :1-2 out jcoupling.dat
run
avg jcoup out avg-jcoupling.dat
EOF

cat << EOF > Karplus.txt.README
  H1'  C1'  N9   C4 : chi adenine
  H1'  C1'  N9   C8 : chi adenine
  C4'  C3'  O3' +P  : epsilon
  C2'  C3'  O3' +P  : epsilon
  H3'  C3'  O3' +P  : epsilin
  P    O5'  C5'  C4': beta
  H4'  C4'  C5'  H5': Gamma, averaged only on Yokoyama1 and Yokoyama2
  H3'  C3'  C4'  H4': Delta, averaged only on Yokoyama1 and Yokoyama2
EOF

cat << EOF > Karplus.txt
 H1'  C1'  N9   C4   4.15  2.06 0.25  -64.30
A5  A3   
 H1'  C1'  N9   C8   4.35  -0.55 0.20  -64.45
A5  A3   
 C4'  C3'  O3' +P   8.13  -2.06 0.40  0
A5  A3   
 C2'  C3'  O3' +P   8.13  -2.06 0.40  -120
A5  A3   
 H3'  C3'  O3' +P   16.23 -5.70 1.03  120
A5  A3  
  P    O5'  C5'  C4'  8.13  -2.06 0.40   0
A3   
 H4'  C4'  C5'  H5'  10.35 -1.0  0     -120
A5    
 H3'  C3'  C4'  H4'  10.35 -1.0  0     120 
A5  A3   
EOF

setenv KARPLUS "./Karplus.txt"
cpptraj -i pt-jcoupling.in > pt-jcoupling.log