diff --git a/scripts/utilities/second_slab.sh b/scripts/utilities/second_slab.sh index a17533c..322bec1 100755 --- a/scripts/utilities/second_slab.sh +++ b/scripts/utilities/second_slab.sh @@ -25,8 +25,8 @@ project_path="${script_path}/../.." if [[ -f "${archive_dir}/${sim_name}_2slab.gro" ]]; then echo "DEBUG: Second slab already added" else + echo "INFO: Adding second slab to box" { - echo "DEBUG: Adding second slab to box" # copy crystal.pdb from initialization cp -np "../1-energy-minimization/crystal.gro" "crystal.gro" || exit 1 @@ -115,7 +115,7 @@ fi if [[ -f "${archive_dir}/topol.top" ]]; then echo "DEBUG: Topology file already updated" else - echo "DEBUG: Updating topology file" + echo "INFO: Updating topology file" { # get all lines [ molecules ] and following from topol.top grep -A 1000 "molecules" topol.top >temp.txt @@ -139,8 +139,10 @@ fi if [[ -f "${archive_dir}/index.ndx" ]]; then echo "DEBUG: Index file already updated" else + echo "INFO: Updating index file" + echo "DEBUG: Python exe: $(which python)" { - python3 "${project_path}/python/twoslab_index.py" \ + python "${project_path}/python/twoslab_index.py" \ -i "index.ndx" \ -g "${sim_name}.gro" \ -o "index.ndx" \