parameterize-it

#!/bin/bash 

#Needed files (in same directory): antechamber_script, tleap-template, convert-to-tinker.py, defs-amber99sb.txt and amber99sb.prm
#Four letter code for 
drug=$1
pdbfile=$drug/$drug.pdb
export ligand_charge=`awk -f get-charge.awk $pdbfile`
cd $drug #scripts are now in ..
echo "Running antechamber"
export ACHOME=/opt/amber14/
export ligand=$drug
../antechamber_script
mv pdb2pqr.ligand.prepi $drug.prepi
echo "Running parmchk"
parmchk2 -i $drug.prepi -o $drug.frcmod -f prepi -p $ACHOME/dat/leap/parm/gaff.dat
echo "Running tleap"
sed -e "s/:rname;/$drug/g" ../tleap-template > $drug.tleap
tleap -f $drug.tleap
echo "converting parameters to tinker format"
#the 2501 and 51 are the starting type number and class number for the converted file; 
#they are set to accommodate the types and classes in amber99sb.prm
export PYTHONPATH=~/lib/python:$PYTHONPATH
drugu=`echo $drug | awk '{print toupper($0)}'`
#on the compute nodes "python" points to "/usr/bin/python" which doesn't seem to be able to handle parmed
#the 2.0 is the cutoff on dihedral force constant for declaring "stiff" bonds
/usr/local/bin/python ../convert-to-tinker.py $drug.prm7 2501 51 $drug.prm
/usr/local/bin/python ../create-defs-solvation2.py $drug.prm7 $drugu 2501 defs-$drug.txt 51 solv-$drug.txt 2.0
#append amber parameters and definitions to create a complete parameter set for the protein-ligand system
cat ../amber99sb.prm $drug.prm > amber99sb-$drug.prm
cat ../defs-amber99sb.txt defs-$drug.txt > defs-amber99sb-$drug.txt
cat ../solvpar-seddd.txt solv-$drug.txt > solvpar-seddd-$drug.txt
cd ..