diff --git a/scripts/aa_index_scripts/new-aa.sh b/scripts/aa_index_scripts/new-aa.sh
new file mode 100755
index 0000000..14e6701
--- /dev/null
+++ b/scripts/aa_index_scripts/new-aa.sh
@@ -0,0 +1,26 @@
+#!/bin/sh
+
+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 ${snp_dir}/output/*mcsm_snps*)
+do
+   echo -n "${i}," >> $aa_outfile
+    python $aa_python $snp_dir/input/pnca_complex.pdb A $i >> $aa_outfile
+done
+# How I want it to run
+#gene = "pncA" # force it to be lowercase
+#chain = "A"
+#mutfile = "/home/tanu/git/Data/output/<gene>_mcsm_snps.csv"
+#mut = for i in mutfile
+
+
+#$1 = "/home/tanu/git/Data/input/<gene>_complex.pdb
+#$2 = chain
+#$3 = mut
+
+#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py  $1 $2 $3
+
diff --git a/scripts/aa_index_scripts/run_aaeg.sh b/scripts/aa_index_scripts/run_aaeg.sh
index edf5fce..f409385 100755
--- a/scripts/aa_index_scripts/run_aaeg.sh
+++ b/scripts/aa_index_scripts/run_aaeg.sh
@@ -1,7 +1,8 @@
+#!/bin/sh
 #python /home/sportelli/Desktop/Important_Code/structural/aaindex/get_scores.py /home/sportelli/Desktop/Project_2_rpoB/leprae/RMLE_B_RFP.pdb C P28A
 #python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/pnca_complex.pdb A L4S
-python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S
-
+#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S
+for i in $(cat /home/tanu/git/Data/pyrazinamide/output/*mcsm_snps*); do echo -n "${i}," >>/home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A $i >> /home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; done
 # How I want it to run
 #drug = "pyrazinamide"
 #gene = "pncA" # force it to be lowercase