#!/bin/csh -f

echo
echo "Step 1"
echo "make the coordinate center at the origin (0,0,0), the tranlation vector is saved in file vector.save. The purpose of this step"
echo "is to avoide the problem of big coordinates causing no space between two values in gaussian output, which makes some programs (such as espgen) fail."

echo "../../../bin/translate -i nad.mol2 -f mol2 -o nad_c.mol2 -c center -a1 0 > vector.out || goto error"
../../../bin/translate -i nad.mol2 -f mol2 -o nad_c.mol2 -c center -a1 0 > vector.out || goto error

echo
echo "Step 2"
echo "run antechamber to generate gaussian gcrt file"
echo "../../../bin/antechamber -i nad_c.mol2 -fi mol2 -o nad.gau -fo gcrt || goto error" 
../../../bin/antechamber -i nad_c.mol2 -fi mol2 -o nad.gau -fo gcrt || goto error 

echo
echo "Step 3"
echo "run gaussian, then generate a new mol2 file (nad_resp.mol2) from the gaussian output file, using the charge flag of '-resp'"
echo "../../../bin/antechamber -i nad.gout -fi gout -fo mol2 -o nad_resp.mol2 -c resp || goto error (not performed)"

echo 
echo "Step 4"
echo "Run antechamber to get RESP charges from the gaussian output file"
echo "../../../bin/antechamber -i nad.gout -fi gout -o nad.ac -fo ac -c resp || goto error" 
../../../bin/antechamber -i nad.gout -fi gout -o nad.ac -fo ac -c resp || goto error 

echo
echo "Step 5"
echo "read in nad.mol2, read resp charges from nad.ac"
echo "../../../bin/antechamber -i nad.mol2 -fi mol2 -o nad_resp.mol2 -fo mol2 -a nad.ac -fa ac -ao crg  || goto error"
../../../bin/antechamber -i nad.mol2 -fi mol2 -o nad_resp.mol2 -fo mol2 -a nad.ac -fa ac -ao crg  || goto error

echo
echo "Step 6"
echo "run parmchk to find missing force field parameters"
echo "../../../bin/parmchk -i nad_resp.mol2 -f mol2 -o frcmod_resp || goto error"
../../../bin/parmchk -i nad_resp.mol2 -f mol2 -o frcmod_resp || goto error

echo
echo "Step 7"
echo "run tleap to generate topology file"
echo "../../../bin/tleap -s -f leap_resp.in > leap_resp.out"
../../../bin/tleap -s -f leap_resp.in > leap_resp.out

echo "../../dacdif -t 1 nad_resp.mol2.save nad_resp.mol2"
../../dacdif -t 1 nad_resp.mol2.save nad_resp.mol2
echo "../../dacdif frcmod_resp.save frcmod_resp"
../../dacdif frcmod_resp.save frcmod_resp
echo "../../dacdif prmtop_resp.save prmtop_resp"
../../dacdif prmtop_resp.save prmtop_resp
echo "../../dacdif prmcrd_resp.save prmcrd_resp"
../../dacdif prmcrd_resp.save prmcrd_resp

/bin/rm -f ANTE* ATOMTYPE.INF BCCTYPE.INF for* FOR* NEWPDB.PDB PREP.INF mopac.in esout QOUT qout punch
exit(0)

error:
echo "  ${0}:  Program error"
exit(1)