create_affinity_vectors

rm -f vec*

lambda=`cat  LAMBDA`

let "index_width = 6 * $lambda"                                   #3 ciphers are added to complex and conf indexes in each iteration.
index_width_ligand=3 


   
     for i in ligand_*.pdbqt
     do
        for j in log*.txt    #inner loop for logs
        do
            b=`basename  $i .pdbqt`
            c=`basename  $j .txt`

            lig_index=`echo "${b:(-$index_width_ligand)}"`
            log_index=`echo "${c:(-$index_width)}"`


            sed -n 28p log$log_index.txt | awk '{print $2;}' >> vec$lig_index


        done
     done