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    Hi, Thank you very much! I did some further test, and I think it isn’t reading the constraints file. Here is the command:./relax.linuxgccrelease -relax:fast -s 00.pdb -database $rodir/rosetta_database -out:pdb -constraints:cst_fa_file constraints_file_name-pdb -constraints:cst_fa_weight 100 -out:nstruct 10.

    Could you tell me why it doesn’t read the constraints file? Or what might be the problem? Thanks!