#!/bin/csh -f
echo
echo
echo
echo
echo "ATTENTION"
echo
echo
echo "The Mulliken charges were generated by mopac in amber10, you may get different result if different QM program is applied"
echo
echo
echo "Step 1"
echo "Run antechamber to calculate the am1-bcc charges"
echo "../../../bin/antechamber -i nad.mol2 -fi mol2 -o nad_bcc.mol2 -fo mol2  -c bcc -s 2 || goto error"
../../../bin/antechamber -i nad.mol2 -fi mol2 -o nad_bcc.mol2 -fo mol2  -c bcc -s 2 || goto error

echo
echo "Step 2"
echo "run parmchk to find missing force field parameters"
echo "../../../bin/parmchk -i nad_bcc.mol2 -f mol2 -o frcmod_bcc || goto error"
../../../bin/parmchk -i nad_bcc.mol2 -f mol2 -o frcmod_bcc || goto error

echo
echo "Step 3"
echo "run tleap to generate topology file"
echo "../../../bin/tleap -s -f leap_bcc.in > leap.out_bcc"
../../../bin/tleap -s -f leap_bcc.in > leap.out_bcc

echo "../../dacdif -t 1 nad_bcc.mol2.save nad_bcc.mol2"
../../dacdif -t 1 nad_bcc.mol2.save nad_bcc.mol2
echo "../../dacdif frcmod_bcc.save frcmod_bcc"
../../dacdif frcmod_bcc.save frcmod_bcc
echo "../../dacdif prmtop_bcc.save prmtop_bcc"
../../dacdif prmtop_bcc.save prmtop_bcc
echo "../../dacdif prmcrd_bcc.save prmcrd_bcc"
../../dacdif prmcrd_bcc.save prmcrd_bcc

/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)