#!/bin/bash

qgrad

while [ -f "INP.NEW" ]; do

 mv INP.NEW BIG.X
 cp FILE.X last.x
 cp BIG.X FILE.X
 rm *.ov
 pdb_dc
 export NOF=`nnof`

for (( i=1; i<=$NOF; i++))
do
echo $i
mkdir tmp 
cp $i.fr.x tmp/FILE.X
cp *TXT tmp
cd tmp
mv F.TXT G.TXT
#make gaussian input:
xinp
g09 FILE.INP FRE.OUT
gg FRE.OUT z
echo AUTO > AUTO
#fix windows version of gaussian:
sed -i 's/|/\\/g' FRE.OUT
#extract gradient:
gar9
cp FILE.GR ../$i.fr.gr
cp FILE.FC ../$i.fr.fc
cd ..
rm -rf tmp
done
cctopt
cctn
qgrad
done