#!/bin/sh
#set -vx

# Create Amber input files for a combined receptor ligand complex
# from a receptor pdb file and a ligand mol2 file.

# The input is:
#    (1)  The receptor pdb filename prefix, ie, the filename without 
#         the .pdb extension.

# The outputs are a pdb file, an Amber prmtop file, and an 
# Amber inpcrd file all for the receptor.

# Scott Brozell and Dave Case , TSRI

if [ $# -eq 1 ]
then
    receptor_pdb_file_prefix=$1
else
    echo "usage:  $0  [receptor_pdb_file_prefix] "
    exit
fi


leapin=`echo $0.leapin.$$ | sed 's@/@_@g'`  # convert pathname into filename
leapin=/tmp/$leapin

output_inpcrd=$receptor_pdb_file_prefix.inpcrd
output_pdb=$receptor_pdb_file_prefix.amber.pdb
output_prmtop=$receptor_pdb_file_prefix.prmtop

cat << EOF > $leapin
 source leaprc.ff94
 x=loadPdb $receptor_pdb_file_prefix.pdb
 savePdb x $output_pdb
 saveAmberParm x $output_prmtop $output_inpcrd
 quit
EOF

DOCKHOME/bin/tleap -s -f $leapin

rm $leapin
mv leap.log $receptor_pdb_file_prefix.log
exit

