Hi,<br>are you sure that the DNA_A and DNA_B groups of atoms are correctly defined in the index.ndx file?<br>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.<br>hope it helps,<br>MG<br><br><div><span class="gmail_quote">On 4/4/06, <b class="gmail_sendername">Super Sayan</b> <<a href="mailto:superbenji83@yahoo.it">superbenji83@yahoo.it</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="direction: ltr;"><div>Hi,</div> <div>I've a little problem: when i type grompp for the full MD, it return an error:
</div> <div> </div><font size="2"> <div>benji@beniamino:~/Desktop/DNA$ grompp -f fullmd_sol.mdp -c minimized_DNA_box_water.gro -p DNA.top -o fullMD.tpr </div> <div>....</div> <div>....</div> <div>....</div><font size="2">
<div>processing index file...</div> <div>Analysing residue names:</div> <div>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat</div> <div>There are: 43015 OTHER residues</div> <div>There are: 0 PROTEIN residues
</div> <div>There are: 0 DNA residues</div> <div>Analysing Other...</div> <div>-------------------------------------------------------</div> <div>Program grompp, VERSION 3.3</div> <div>Source code file: readir.c, line: 775
</div> <div>Fatal error:</div> <div>Group DNA_A not found in indexfile.</div> <div>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.</div> <div>In
that case use the '-n' option.</div> <div> </div> <div>but also with the -n option there aren't any differences.</div> <div>in the .mdp file i used "DNA_A" "DNA_B" "SOL" as group;</div>
<div>DNA_A and DNA_B are .itp files, and i've also DNA_posre_A.itp DNA_posre_B.itp files.</div> <div> </div> <div>what can i do?</div> <div>thanks very much</div> <div>PS:i hope that i've been clear.</div> <div>Beniamino
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