Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue —(CH2-CF2-CF2-CFCl)— It's not the polymer structure. f2311-new.pdb <http://gromacs.5086.n6.nabble.com/file/n5006334/f2311-new.pdb>
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