CHARMMPDB

#This script converts a .xyz file to a CHARMM formatted .pdb file
#If the files are not formatted properly, CHARMM calculations will crash

#!/bin/bash

# f is using Babel to convert .xyz to .pdb
# g is using grep to remove lines w/a particular phrase
# h is for converting HETATM to ATOM  (plus two spaces)
# i is for removing the 11th column, but retaining the table format (otherwise the file is no good)
# j is for adding a new 11th column w/the correct formatting (six spaces)

module load Babel/2.3.2

mkdir backup

cp *xyz backup

for f in *xyz
do

        babel $f -opdb -m

        mv *pdb new.pdb

done

for g in new.pdb
do

        grep -v "\bCOMPND\b" $g > $g.tmp
        grep -v "\bAUTHOR\b" $g.tmp > $g.tmp.tmp
        grep -v "\bCONECT\b" $g.tmp.tmp > $g.tmp.tmp.tmp
        grep -v "\bMASTER\b" $g.tmp.tmp.tmp > $g.tmp.tmp.tmp.tmp
        grep -v "\bEND\b" $g.tmp.tmp.tmp.tmp > new.pdb

        rm -f $g.tmp $g.tmp.tmp $g.tmp.tmp.tmp $g.tmp.tmp.tmp.tmp

done

for h in new.pdb
do

        sed -i -e 's/HETATM/ATOM  /g' $h

done

for i in new.pdb
do

        awk '{ printf "%-10s%-3d%-4s%-8s%-1d      %6.3f  %6.3f  %6.3f  %-4.2f  %-4.2f\n", $1,$2,$3,$4,$5,$6,$7,$8,$9,$10 }' new.pdb > new.edit

        mv new.edit new.pdb

done

for j in new.pdb
do

        sed 's/$/      SUB/' new.pdb > new.tmp

        mv new.tmp $f
        mv $f tropcsubstrate.pdb

done

rm -f new.pdb