Hi Marzieh, do you have any group named as Protein in nvt.mdp, e.g. tc-grps? The covalent bond you created might be between protein atoms I guess. Could you follow the tips given by grompp, namely supply an index file that contain the group atom index of each group specified in your mdp file, and run grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr?
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