[gmx-users] grompp error

[MGiò]

Hi,
are you sure that the DNA_A and DNA_B groups of atoms are correctly defined
in the index.ndx file?
Actually, it seems that grompp couldn't find them defined because they
aren't default groups, so you have to generate a proper user-defined
index.ndx file using make_ndx.
hope it helps,
MG

On 4/4/06, Super Sayan <superbenji83 at yahoo.it> wrote:
>
> Hi,
> I've a little problem: when i type grompp for the full MD, it return an
> error:
>
> benji at beniamino:~/Desktop/DNA$ grompp -f fullmd_sol.mdp -c
> minimized_DNA_box_water.gro -p DNA.top -o fullMD.tpr
> ....
> ....
> ....
> processing index file...
> Analysing residue names:
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are: 43015 OTHER residues
> There are: 0 PROTEIN residues
> There are: 0 DNA residues
> Analysing Other...
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: readir.c, line: 775
> Fatal error:
> Group DNA_A not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the
> '-n' option of grompp.
> In that case use the '-n' option.
>
> but also with the -n option there aren't any differences.
> in the .mdp file i used "DNA_A" "DNA_B" "SOL" as group;
> DNA_A and DNA_B are .itp files, and i've also DNA_posre_A.itp
> DNA_posre_B.itp files.
>
> what can i do?
> thanks very much
> PS:i hope that i've been clear.
> Beniamino
>
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