# apbs calculation for biotin streptavin complex

curr=`pwd`

cd /bluefin1/park/Programs/pdb2pqr-1.5/
cp /bluefin1/park/MD/toppar/biotah2.pqr biot.pqr

for i in {0..402};
do
	if [ -f /tmp/m54e/cha/a.pdb.$i ];
	then
	    echo "======================================="
	    echo "Computing PDQ2PQR: 0"
	    grep "^ATOM" /tmp/m54e/cha/a.pdb.$i > temp.pdb
	    python pdb2pqr.py --ff=parse temp.pdb /tmp/m54e/cha/a.pqr.$i

	    grep "^ATOM" /tmp/m54e/chb/b.pdb.$i | cut -c-54 > temp.pqr
	    perl ~/scripts/combq.pl biot.pqr temp.pqr > /tmp/m54e/chb/b.pqr.$i

	    perl ~/scripts/add.pl /tmp/m54e/cha/a.pqr.$i /tmp/m54e/chb/b.pqr.$i > /tmp/m54e/comp/ab.pqr.$i
	fi
done

cd $curr