removed `/scratch/xiaobo/3272/xam-8058097.13/working/protonate/xam-protonated-manual.ism' removed `/scratch/xiaobo/3272/xam-8058097.13/working/protonate/xam-protomers-expanded.ism' removed `/scratch/xiaobo/3272/xam-8058097.13/working/protonate/xam-protomers.ism' removed directory: `/scratch/xiaobo/3272/xam-8058097.13/working/protonate' removed `/scratch/xiaobo/3272/xam-8058097.13/working/input-smiles.ism'