[gmx-users] Index error

[Collins Nganou]

Dear Users,

I would like to know if anyone may help me understand how to update the
index file.
I am trying to simulate a dna in solution.
I have relaxed a Solvent with attached min.mdp file without problem. in
the second step I was intended to relax SOL + Na  DNA with 20ps.mdp. But
the index file did not work.
I have trying to generate an index file using the file.gro from min.mdp but
it doesn't work.

Below is the obtained error.

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning H bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning H bonds into constraints...
Velocities were taken from a Maxwell distribution at 10 K

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Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line:
1332

Fatal error:
Group NA+SOL referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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I am looking forward to have any suggestion that might help me in this
case.

I wish all of you a wonderful day.

Collins