[gmx-users] error group protein not found

[Jin Zhang]

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?

Regards,
Jin