Updated master directory to include the neccessary filestructure, sub…

…mission script, and instructions.

batch/params.txt

@@ -0,0 +1,7 @@
+center_x =
+center_y =
+center_z =
+
+size_x =
+size_y =
+size_z =

batch/submit.sh

@@ -0,0 +1,35 @@
+echo "Batch Submission Script for AutoDock Vina, Bhavesh Ashok"
+echo "github.com/bhaveshashok/AutoDockVina-BatchSubmission/"
+echo "Please acknowledge your use of this script in your publication using the guidelines on the GitHub page!"
+
+
+echo "Generating Configurations:"
+for ligand in $(ls -1 $1/*.pdbqt)
+do
+    #echo $ligand
+    name=$(echo $ligand | sed 's/.*\///;s/\..*//')
+    echo "Generating configuration for $name ..."
+    mkdir -p "$name"
+    cp $ligand $name
+    cp $2 $name
+    ligandfname=$(echo $ligand | sed 's/.*\///')
+    echo -en "receptor = $2\nligand = $ligandfname\n\n" > "$name/${name}_conf.txt"
+    cat $3 >> "$name/${name}_conf.txt"
+    echo "Done!"
+done
+
+echo "Success: Configurations generated"
+
+echo "Submitting to Vina:"
+for ligand in $(ls -1 $1/*.pdbqt)
+do
+    name=$(echo $ligand | sed 's/.*\///;s/\..*//')
+    pushd $name
+    echo "Docking $name ..."
+    $("$4" --config "${name}_conf.txt" --log "${name}_log.txt")
+    popd
+    rm $ligand
+    echo "Done!"
+done
+
+echo "Success: Batch docked"