Fix grep Error: 'invalid option -- '.' in Linux

The command you are running is not valid. The error message 'grep: invalid option -- '.' suggests that the option you used after "xargs" is not recognized. To fix this issue, you can modify the command as follows:

grep -rl '626.89' /mnt/hpc/home/zhengpu/srb/enzdes_5/*/*complex__DE_2.pdb | xargs -I {} grep -l '-55.06' {}

This command will search for files containing '626.89' in the specified directory and then search within those files for files containing '-55.06'.