create_Vina_config_file

# Input parameters: ligand index, complex index, config file index
# Output parameter: Vina config file

lig_index=$1
comp_index=$2
conf_index=$3

source $vini_dir/sourceme

$MGLBIN/pythonsh $MGLUTILS/prepare_gpf4.py -l ligand_${lig_index}.pdbqt -r complex_${comp_index}.pdbqt -o complex_${comp_index}.gpf

sed -i '1s/^/parameter_file AD4_parameters.dat\n/' complex_${comp_index}.gpf #Add <parameter_file AD4_parameters.dat> as the 1st line in *.gpf

#$vini_dir/autogrid4 -p complex_${comp_index}.gpf -l complex_${comp_index}.glg  2> /dev/null | tee -a $WORKDIR/${comp_index}/stats #Create grid maps and redirects standard error to device null
$vini_dir/autogrid4 -p complex_${comp_index}.gpf -l complex_${comp_index}.glg #Create grid maps

if  [ -e complex_${comp_index}.maps.fld ]
then
    line=`head -n 9 complex_${comp_index}.maps.fld | tail -1` #get xyz coordinates
    echo $line > tempor1
    grep CENTER tempor1 > tempor2
    count=`wc -c < tempor2`
    one=1
    if [ $count -eq $NULL ]
    then
        center_x=0
        center_y=0
        center_z=0
    else
        center_x=`echo $line | awk '{print $2}'`
        center_y=`echo $line | awk '{print $3}'`
        center_z=`echo $line | awk '{print $4}'`
    fi
else
    center_x=0
    center_y=0
    center_z=0
fi

printf "%s%s\n\n%s%s\n\n%s%s\n" "center_x = " "$center_x" "center_y = " "$center_y" "center_z = " "$center_z" > conf_${conf_index}.txt