diff --git a/scripts/aa_index_scripts/new-aa.sh b/scripts/aa_index_scripts/new-aa.sh
index 14e6701..6bbd144 100755
--- a/scripts/aa_index_scripts/new-aa.sh
+++ b/scripts/aa_index_scripts/new-aa.sh
@@ -1,15 +1,16 @@
 #!/bin/sh
+drug=${1:-pyrazinamide}
+gene=${2:-pnca}
 
-drug="pyrazinamide"
-gene="pnca"
 aa_python="/home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py"
 snp_dir="/home/tanu/git/Data/${drug}"
 aa_outfile="/home/tanu/git/Data/${drug}/output/aa_index/${gene}_aa"
 
-for i in $(cat ${snp_dir}/output/*mcsm_snps*)
+echo "Running for drug: ${drug} and gene ${gene}. Output to: ${aa_outfile}"
+for i in $(cat ${snp_dir}/output/${gene}_mcsm_formatted_snps.csv)
 do
    echo -n "${i}," >> $aa_outfile
-    python $aa_python $snp_dir/input/pnca_complex.pdb A $i >> $aa_outfile
+    python $aa_python $snp_dir/input/${gene}_complex.pdb A $i >> $aa_outfile
 done
 # How I want it to run
 #gene = "pncA" # force it to be lowercase