#!/bin/bash
#
# Generated with Raccoon | AutoDockVS
#

#### PBS jobs parametersCPUT="24:00:00"
WALLT="24:00:00"
#
# There should be no reason
# for changing the following values
NODES=1
PPN=1
MEM=512mb


### CUSTOM VARIABLES
#
# use the following line to set special options (e.g. specific queues)
#OPT="-q MyPriorQueue"
OPT=""


# Paths for executables on the cluster
# Modify them to specify custom executables to be used
QSUB="qsub"
AUTODOCK="autodock4"

AUTOGRID="autogrid4"

# Special path to move into before running
# the screening. This is very system-specific,
# so unless you're know what are you doing,
# leave it as it is
WORKING_PATH=`pwd`



##################################################################################################
##################################################################################################
####### There should be no need to modify anything below this line ###############################
##################################################################################################
##################################################################################################


#
#

type $AUTODOCK &> /dev/null || {
        echo -e "nError: the file [$AUTODOCK] doesn't exist or is not executablen";
        echo -e "Try to specify the full path to the executable of the AutoDock binary in the script";
        echo -e "( i.e. AUTODOCK=/usr/bin/autodock4 )nn";
        echo -e " [ virtuals screening submission aborted]n"
        exit 1; }

type $AUTOGRID &> /dev/null || {
        echo -e "nError: the file [$AUTOGRID] doesn't exist or is not executablen";
        echo -e "Try to specify the full path to the executable of the AutoGrid binary in the script";
        echo -e "( i.e. AUTOGRID=/usr/bin/autogrid4 )nn";
        echo -e " [ virtuals screening submission aborted]n"
        exit 1; }

type $QSUB &> /dev/null || {
        echo -e "nError: the file [$QSUB] doesn't exist or is not executablen";
        echo -e "Try to specify the full path to the executable of the Qsub command binary in the script";
        echo -e "( i.e. QSUB=/usr/bin/qsub )nn";
        echo -e " [ virtuals screening submission aborted]n"
        exit 1; }

echo Starting submission...
for NAME in `cat jobs_list`
    do
        cd $NAME
        echo "#!/bin/bash" > $NAME.job
        echo "cd $WORKING_PATH/$NAME" >> $NAME.job
        echo "$AUTOGRID -p *.gpf -l grid_out.glg" >> $NAME.job
        echo "$AUTODOCK -p $NAME.dpf -l $NAME.dlg" >> $NAME.job
        chmod +x $NAME.job
        echo -n "Submitting $NAME : "
        $QSUB $OPT -l cput=$CPUT -l nodes=1:ppn=1 -l walltime=$WALLT -l mem=$MEM $NAME.job
        cd ..
done