#!/bin/sh

. ../program_error.sh

DACDIF=../dacdif
tleap=./tleap
leaprc=$AMBERHOME/dat/leap/cmd/oldff/leaprc.ff10
ion_params=$AMBERHOME/dat/leap/parm/frcmod.ionsjc_tip3p
dry_prefix=trx
wet_prefix=trx.solv

cat > leap.in << EOF
# Source the force field
source $leaprc
loadamberparams $ion_params

# Change the default PB radii
set default pbradii mbondi2

# Load the PDB
prot = loadpdb trx.pdb

# Save a non-solvated topology
saveamberparm prot $dry_prefix.parm7 $dry_prefix.rst7

# Solvate, add ions, and save a new topology file
solvateoct prot TIP3PBOX 10.0

addions prot NA 0
addions prot CL 0

saveamberparm prot $wet_prefix.parm7 $wet_prefix.rst7

# quit
quit
EOF

echo ""
echo "         Creating a new-style (Amber 7) topology file "
echo ""

$tleap -f leap.in > leap2.log

$DACDIF $dry_prefix.parm7.save $dry_prefix.parm7
$DACDIF $wet_prefix.parm7.save $wet_prefix.parm7

/bin/rm -f leap.in leap.log leap2.log $dry_prefix.rst7 $wet_prefix.rst7