<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</DIV></FONT></FONT><p>
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