Antechamber cannot be run in parallel in the same folder.

[diegoenry]

I just realized that antechamber can not be executed at the concurrently at the same folder.

For each ligand it generates a number of temporary files with the same name

Quick solution could be running from a temporary folder, example here:
dbarreto@hpc-login1:~/ChemFlow_paper/Benchmark_meso$ vim LigFlow_names.bash

cd $(mktemp -d ) ; antechamber -i ${RUNDIR}/${LIGAND}.mol2 ...

[diegoenry]

Still to be fixed. the previous solution did not work, as XARGS runs "mktemp -d" at exactly the same time meaning the same foldername will be generated.

A quick fix was to create a temp folder for each ligand. anyway, this is NOT implemented in the code.