[gmx-users] grompp fatal error in GROMACS version 4.5.7

[Agnivo Gosai]

Dear GROMACS users

I received the following error while running grompp to prepare the .tpr
file before the initial energy minimization of my system.






*Fatal error:Group DNA_chain_D referenced in the .mdp file was not found in
the index file.Group names must match either [moleculetype] names or custom
index groupnames, in which case you must supply an index file to the '-n'
optionof grompp.*
I used the following few commands in succession before this :-
(1) pdb2gmx -f 1HAO.pdb -o complex.gro -p complex.top
(2) editconf -f complex.gro -o complex_box.gro -bt dodecahedron -d 1.0
(3) genbox -cp complex_box.gro -cs spc216.gro -p complex.top -o
complex_solv.gro
(4) grompp -f em.mdp -c complex_solv.gro -p complex.top -o ions.tpr
(5) genion -s ions.tpr -o complex_ions.gro -p complex.top -pname NA -nname
CL -neutral -conc 0.1
(6) grompp -f em_real.mdp -c complex_ions.gro -p complex.top -o em.tpr

After command (6) error is coming.

In em.mdp file , at step (4) I have , "energygrps = system" and in
em_real.mdp file at step (6) I have ," nenergygrps    = DNA_chain_D
Protein_chain_L Protein_chain_H . ( Note : These files I gathered from Dr.
Lemkuls tutorial on protein-ligand system )

Also my complex.top file has the following :-
; Include chain topologies
#include "complex_DNA_chain_D.itp"
#include "complex_Protein_chain_L.itp"
#include "complex_Protein_chain_H.itp"
...........................................................
...........................................................
[ molecules ]
; Compound        #mols
DNA_chain_D         1
Protein_chain_L     1
Protein_chain_H     1
SOL         13578
NA               39
CL               28

and ,

"complex_DNA_chain_D.itp" has the following :-
[ moleculetype ]
; Name            nrexcl
DNA_chain_D         3

Similar statements are available in the other two .itp files mentioned in
the complex.top file. Now I am unable to understand what the error
statement means by specifying "index file" ??
Please shed some light upon this. I have also consulted the error section
of the GROMACS documentation but could not understand.

Thanks & Regards,

Agnivo Gosai
Grad. Student , Iowa State University