[gmx-users] grompp errors..

[Ali Alizadeh]

Dear All users

I have a system with 3 layers,
when i run grompp program, encounter with this error.
First and 3th layer is the same, and middle layer is water. what's
this error about?
and i have another question about make_ndx, How to make index the same
atoms with different res number  in .gro file?

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Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'nstcheckpoint'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Ion'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion2'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Analysing residue names:
There are:  1183        Ion residues
There are:  1830      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...
Number of degrees of freedom in T-Coupling group System is 23990.00

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1320

Fatal error:
Group 1 not found in 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.