#!/usr/bin/env bash

out_dir="$(basename ${0})"
out_dir="${out_dir%%.*}"

# create array of system names

ARR1=()
for i in 1-concat/individual/*/*/ ; do
    ARR1+=($(basename ${i}))
done

# make directory and create ndx files

mkdir -p "${out_dir}"

while read system; do
    ARR2=("${out_dir}/individual/*/${system}/${system}-*.pdb")
    ARR3=("${out_dir}/individual/*/${system}/${system}.ndx")
    gmx make_ndx -f ${ARR2[1]} -n ${ARR3[1]} -o "${out_dir}/${system}.ndx"
done < <(echo ${ARR1[@]} | tr " " "\n" | sort -u)