[gmx-users] grompp error

Super Sayan superbenji83 at yahoo.it
Tue Apr 4 14:32:50 CEST 2006

  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.

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