#!/bin/csh -f

# Step 1 - Generate an ac file from a gaussian output file

../../../bin/antechamber -fi gout -fo ac -i ala_conf1.gout -o ala.ac  \
   >& antechamber.out || goto error

# Step 2 - Extract ESP for both conformations and merge them to a file called
# ala.esp 

../../../bin/espgen -i ala_conf1.gout -o ala_conf1.esp >& espgen.out
../../../bin/espgen -i ala_conf2.gout -o ala_conf2.esp >& espgen.out

/bin/rm -f ala.esp 
cat ala_conf1.esp ala_conf2.esp > ala.esp 

# Step 3 - Manually prepare the input file for residuegen, please see
# residuegen.input 

# Step 4 - Run residuegen to get the amino-acid-like residue topology 

../../../bin/residuegen residuegen.input >& residuegen.out

# By the way, the program itself does not know this molecule is an amino acid
# residue, you can use this program to generate residue topologies for nucleic
# acids and other polymers as well

../../dacdif -t 1 ala.ac.save ala.ac
../../dacdif -t 1 ala.esp.save ala.esp
../../dacdif -s -t 1 ala.prep.save ala.prep

exit(0)

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