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 <[EMAIL PROTECTED]> wrote:
Hi,I've a little problem: when i type grompp for the full MD, it return an error:[EMAIL PROTECTED]:~/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.datThere are: 43015 OTHER residuesThere are: 0 PROTEIN residuesThere are: 0 DNA residuesAnalysing Other...-------------------------------------------------------Program grompp, VERSION 3.3Source code file: readir.c, line: 775Fatal 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 muchPS:i hope that i've been clear.Beniamino
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