run_module5.sh

#!/bin/bash

m1=$(awk -v var=1 'NR==var {print $1}' names.dat)
m2=$(awk -v var=2 'NR==var {print $1}' names.dat)
num_configs=
amber_name=$(awk -v var=1 'NR==var {print $2}' modules.dat)
vmd_name=$(awk -v var=2 'NR==var {print $2}' modules.dat)
matlab_name=$(awk -v var=3 'NR==var {print $2}' modules.dat)

cd module_5/correction/
cp calc_corrections.sh calc_corrections_t.sh
sed -i "s/MOLEC1/$m1/g" calc_corrections_t.sh
sed -i "s/MOLEC2/$m2/g" calc_corrections_t.sh
sed -i "s/CONF_NUM/num_configs/g" calc_corrections_t.sh
sed -i "s/AMBER_MODULE_NAME/amber_name/g" calc_corrections_t.sh
sed -i "s/VMD_MODULE_NAME/vmd_name/g" calc_corrections_t.sh
bash calc_corrections_t.sh
rm calc_corrections_t.sh

cd ..
cp km_calc.sh km_calc_t.sh
sed -i "s/CONF_NUM/$num_configs/g" km_calc_t.sh
sed -i "s/MATLAB_MODULE_NAME/matlab_name/g" km_calc_t.sh
bash km_calc_t.sh
rm km_calc_t.sh
cd ..