#!/bin/sh
echo "WARNING: lmodprmtop is now deprecated and will be removed in future"
echo "         versions of AmberTools. Please use the 'lmod' action in ParmEd"
echo "         instead"

input=$1
output=$2

if [ ! "$input" ] || [ ! "$output" ]; then echo 'Usage: lmodprmtop input_prmtop output_prmtop'; exit; fi

#sed -e '/LENNARD_JONES_ACOEF/,/LENNARD_JONES_BCOEF/ s/0.00000000E+00/1.00000000E+03/g' $input >$output 

# Go through ParmEd instead, since it is more robust and does not depend on flag
# ordering in the topology file (and it also works -- I have verified that
# they give the same topologies). Oh, and it also works on old-style topologies

# This also has safer topology overwriting, if that is desired.
$AMBERHOME/bin/parmed.py -n -p $1 << EOF
setOverwrite True
lmod
parmout $2
EOF