#!/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 start 1 stop 1000

dihedral :1@H1' :1@C1' :1@N9 :1@C4 out chi1.dat
dihedral :1@C4' :1@C3' :1@O3' :2@P out ep1.dat
dihedral :2@C4' :2@C3' :2@O3' :2@P out ep1.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
  P    O5'  C5'  C4': beta
EOF

cat << EOF > Karplus.txt
 H1'  C1'  N9   C4   4.15  2.05  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
  P    O5'  C5'  C4'  8.13  -2.06 0.40   0
A3   
EOF

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