#!/bin/csh -f

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

echo 
echo ../../../bin/translate -i nad.mol2 -f mol2 -o nad_c.mol2 -c center -a1 0 ">" vector.save  
echo 

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

echo  Step 2
echo  run antechamber to generate gaussian gcrt file

echo
echo ../../../bin/antechamber -i nad_c.mol2 -fi mol2 -o nad.gau -fo gcrt ">" antechamber.out
echo 

../../../bin/antechamber -i nad_c.mol2 -fi mol2 -o nad.gau -fo gcrt \
   >& antechamber.out || goto error 

echo  Step 3
echo  run gaussian, then generate a new mol2 file "(nad_c.mol2)" from the gaussian
echo  output file, using the charge flag of '-resp' if ESP were printed out in the
echo  gaussian output file.
 
echo
echo ../../../bin/antechamber -i nad.gout -fi gout -fo mol2 -o nad_c.mol2 -c resp ">>" antechamber.out
echo 
../../../bin/antechamber -i nad.gout -fi gout -fo mol2 -o nad_c.mol2 -c resp \
   >& antechamber.out || goto error 
echo  Step 4
echo  since the coordinates have been translated, one may translate the molecule
echo  back using the 'translate' program with the saved vectors or do a Least-square fitting 
echo
echo translate
echo 
echo ../../../bin/translate -i nad_c.mol2 -f mol2 -o nad.mol2 -c translate -vx -45.1416 -vy -52.7378 -vz -78.7059 ">" translate.out 
echo 
../../../bin/translate -i nad_c.mol2 -f mol2 -o nad.mol2 -c translate \
   -vx -45.1416 -vy -52.7378 -vz -78.7059 >& translate.out || goto error
echo lsfit
echo
echo ../../../bin/translate -i nad_c.mol2 -f mol2 -o nad.mol2 -c match -r nad.mol2 
echo 
../../../bin/translate -i nad_c.mol2 -f mol2 -o nad.mol2 -c match \
   -r nad.mol2 || goto error
echo 
echo  Step 5
echo If one wants to use am1-bcc charge, skip the above steps and just run the
echo  following command
echo 
echo ../../../bin/antechamber -i nad.mol2 -fi mol2 -o nad_c.mol2 -fo mol2 -c bcc -s 2 ">>" antechamber.out 
echo  

../../../bin/antechamber -i nad.mol2 -fi mol2 -o nad_c.mol2 -fo mol2  \
   -c bcc -s 2 >& antechamber.out || goto error

echo  Step 6
echo  run parmchk to find missing force field parameters
echo
echo ../../../bin/parmchk -i nad_c.mol2 -f mol2 -o frcmod 
echo
../../../bin/parmchk -i nad_c.mol2 -f mol2 -o frcmod || goto error
echo  Step 7
echo  run tleap to generate topology file
echo
echo ../../../bin/tleap -s -f leap.in ">" leap.out
echo
../../../bin/tleap -s -f leap.in > leap.out

../../dacdif -t 1 prmtop.save prmtop 
../../dacdif -t 1 prmcrd.save prmcrd 
../../dacdif -t 1 frcmod.save frcmod 
../../dacdif nad.mol2.save nad.mol2

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

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