#!/usr/bin/env bash

HERE=$PWD
cd toppar

cat > tmp.pgn << EOF
topology top.rtf
segment ION {
  residue 1 SOD
  residue 2 SOD
}
writepsf lambda0.psf
EOF
psfgen < tmp.pgn

cat > lambda0.pdb << EOF
ATOM      1  SOD SOD     1       0.000   0.000   0.000  1.00  0.00      ION  
ATOM      2  SOD SOD     1      -3.000   0.000   0.000  1.00  0.00      ION
END
EOF

cat > tmp.pgn << EOF
topology top.rtf
segment ION {
  residue 1 SOD
  residue 2 CLA
}
writepsf lambda1.psf
EOF
psfgen < tmp.pgn

cat > lambda1.pdb << EOF
ATOM      1  SOD SOD     1       0.000   0.000   0.000  1.00  0.00      ION
ATOM      2  CLA CLA     1       3.000   0.000   0.000  1.00  0.00      ION
END
EOF

cat > tmp.pgn << EOF
topology top.rtf
segment ION {
  residue 1 SOD
  residue 2 SOD
  residue 3 CLA
}
writepsf dualtopo.psf
EOF
psfgen < tmp.pgn

cat > dualtopo.pdb << EOF
ATOM      1  SOD SOD     1       0.000   0.000   0.000  1.00  0.00      ION
ATOM      2  CLA CLA     1       3.000   0.000   0.000  1.00 -1.00      ION
ATOM      3  SOD SOD     1      -3.000   0.000   0.000  1.00  1.00      ION
END
EOF

cd $HERE

