There is zinc in a catalytic site. So, I merge Protein_Zn_Ligand by using command:

gmx make_ndx -f em.gro -o index.ndx

> 1 | 13 | 14

> q

and set tc_grps = Protein_ZN_JZ4 Water_and_ions in .mdp file.

When I run the Equilibration step, I get the error:

Fatal error:

Atom 7006 in multiple T-Coupling groups (1 and 2)

0 System : 176703 atoms

1 Protein : 7005 atoms

2 Protein-H : 5535 atoms

3 C-alpha : 723 atoms

4 Backbone : 2169 atoms

5 MainChain : 2893 atoms

6 MainChain+Cb : 3556 atoms

7 MainChain+H : 3578 atoms

8 SideChain : 3427 atoms

9 SideChain-H : 2642 atoms

10 Prot-Masses : 7005 atoms

11 non-Protein : 169698 atoms

12 Ion : 348 atoms

13 ZN : 1 atoms

14 JZ4 : 42 atoms

15 NA : 183 atoms

16 CL : 164 atoms

17 Other : 42 atoms

18 ZN : 1 atoms

19 JZ4 : 42 atoms

20 NA : 183 atoms

21 CL : 164 atoms

22 Water : 169308 atoms

23 SOL : 169308 atoms

24 non-Water : 7395 atoms

25 Water_and_ions : 169656 atoms

nr : group ! 'name' nr name 'splitch' nr Enter: list groups

'a': atom & 'del' nr 'splitres' nr 'l': list residues

't': atom type | 'keep' nr 'splitat' nr 'h': help

'r': residue 'res' nr 'chain' char

"name": group 'case': case sensitive 'q': save and quit

'ri': residue index

> 1 | 13 | 14

Copied index group 1 'Protein'

Copied index group 13 'ZN'

Merged two groups with OR: 7005 1 -> 7006

Copied index group 14 'JZ4'

Merged two groups with OR: 7006 42 -> 7048

26 Protein_ZN_JZ4 : 7048 atoms

> q

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html